Environmental regulation of lateral root emergence in Medicago truncatula requires the HD-Zip I transcription factor HB1

GhHDZ76, a cotton HD-Zip transcription factor, involved in regulating the initiation and early elongation of cotton fiber development in G. hirsutum

In this study, the whole HD-Zip family members of G. hirsutum were identified, and GhHDZ76 was classified into the HD-Zip IV subgroup. GhHDZ76 was predominantly expressed in the 0-5 DPA of fiber development stage and localized in the nucleus. Overexpression of GhHDZ76 significantly increased the length and density of trichomes in Arabidopsis thaliana. The fiber length of GhHDZ76 knockout lines by CRISPR/Cas9 was significantly shorter than WT at the early elongation and mature stage, indicating that GhHDZ76 positively regulate the fiber elongation. Scanning electron microscopy showed that the number of ovule surface protrusion of 0 DPA of GhHDZ76 knockout lines was significantly lower than WT, suggesting that GhHDZ76 can also promote the initiation of fiber development. The transcript level of GhWRKY16, GhRDL1, GhEXPA1 and GhMYB25 genes related to fiber initiation and elongation in GhHDZ76 knockout lines were significantly decreased. Yeast two-hybrid and Luciferase complementation imaging (LCI) assays showed that GhHDZ76 can interact with GhWRKY16 directly. As a transcription factor, GhHDZ76 has transcriptional activation activity, which could bind to L1-box elements of the promoters of GhRDL1 and GhEXPA1. Double luciferase reporter assay showed that the GhWRKY16 could enhance the transcriptional activity of GhHDZ76 to pGhRDL1, but it did not promote the transcriptional activity of GhHDZ76 to pGhEXPA1. GhHDZ76 protein may also promote the transcriptional activity of GhWRKY16 to the downstream target gene GhMYB25. Our results provided a new gene resource for fiber development and a theoretical basis for the genetic improvement of cotton fiber quality.

A lateral organ boundaries domain transcription factor acts downstream of the auxin response factor 2 to control nodulation and root architecture in Medicago truncatula

Legume plants develop two types of root postembryonic organs, lateral roots and symbiotic nodules, using shared regulatory components. The module composed by the microRNA390, the Trans-Acting SIRNA3 (TAS3) RNA and the Auxin Response Factors (ARF)2, ARF3, and ARF4 (miR390/TAS3/ARFs) mediates the control of both lateral roots and symbiotic nodules in legumes. Here, a transcriptomic approach identified a member of the Lateral Organ Boundaries Domain (LBD) family of transcription factors in Medicago truncatula, designated MtLBD17/29a, which is regulated by the miR390/TAS3/ARFs module. ChIP-PCR experiments evidenced that MtARF2 binds to an Auxin Response Element present in the MtLBD17/29a promoter. MtLBD17/29a is expressed in root meristems, lateral root primordia, and noninfected cells of symbiotic nodules. Knockdown of MtLBD17/29a reduced the length of primary and lateral roots and enhanced lateral root formation, whereas overexpression of MtLBD17/29a produced the opposite phenotype. Interestingly, both knockdown and overexpression of MtLBD17/29a reduced nodule number and infection events and impaired the induction of the symbiotic genes Nodulation Signaling Pathway (NSP) 1 and 2. Our results demonstrate that MtLBD17/29a is regulated by the miR390/TAS3/ARFs module and a direct target of MtARF2, revealing a new lateral root regulatory hub recruited by legumes to act in the root nodule symbiotic program.

Functional and regulatory diversity of homeobox-leucine zipper transcription factors BnaHB6 under dehydration and salt stress in Brassica napus L

The plant-specific homeodomain-leucine zipper I subfamily is involved in the regulation of various biological processes, particularly growth, development and stress response. In the present study, we characterized four BnaHB6 homologues from Brassica napus. All BnaHB6 proteins have transcriptional activation activity. Structural and functional data indicate the complex role of BnaHB6 genes in regulating biological processes, with some functions conserved and others diverged. Transcriptional analyzes revealed that they are induced in a similar manner in different tissues but show different expression patterns in response to stress and circadian rhythm. Only the BnaA09HB6 and BnaC08HB6 genes are expressed under dehydration and salt stress, and in darkness. The partial transcriptional overlap of BnaHB6s with the evolutionarily related genes BnaHB5 and BnaHB16 was also observed. Transgenic Arabidopsis thaliana plants expressing a single proBnaHB6::GUS partially confirmed the expression results. Bioinformatic analysis allowed the identification of TF-binding sites in the BnaHB6 promoters that may control their expression under stress and circadian rhythm. ChIP-qPCR analysis revealed that BnaA09HB6 and BnaC08HB6 bind directly to the promoters of the target genes BnaABF4 and BnaDREB2A. Comparison of their expression patterns in the WT plants and the bnac08hb6 mutant showed that BnaC08HB6 positively regulates the expression of the BnaABF4 and BnaDREB2A genes under dehydration and salt stress. We conclude that four BnaHB6 homologues have distinct functions in response to stress despite high sequence similarity, possibly indicating different binding preferences with BnaABF4 and BnaDREB2A. We hypothesize that BnaC08HB6 and BnaA09HB6 function in a complex regulatory network under stress.

In silico genome-wide analysis of homeodomain-leucine zipper transcription factors in Cannabis sativa L

HD-Zip (Homeodomain-Leucine Zipper) is a family of transcription factors unique to higher plants and plays a vital role in plant growth and development. Increasing research results show that HD-Zip transcription factors are widely involved in many life processes in plants. However, the HD-Zip transcription factor for cannabis, a valuable crop, has not yet been identified. The sequence characteristics, chromosome localization, system evolution, conservative motif, gene structure, and gene expression of the HD-Zip transcription factor in the cannabis genome were systematically studied. Real-time quantitative polymerase chain reaction (qRT-PCR) was used to verify its function. The results showed that cannabis contained 33 HD-Zip gene members. The number of amino acids is 136-849aa, the isoelectric point is 4.54-9.04, and the molecular weight is 23264.32-93147.87Da. Many cis-acting elements are corresponding to hormone and abiotic stress in the HD-Zip family promoter area of cannabis. Sequencing of the transcriptome at 5 tissue sites of hemp, stems, leaves, bracts, and seeds showed similar levels of expression of 33 members of the HD-Zip gene family at 5 tissue sites. Bioinformatics results show that HD-Zip expression is tissue-specific and may be influenced by hormones and environmental factors. This lays a foundation for further research on the gene function of HD-Zip.

HD-Zip I protein LlHOX6 antagonizes homeobox protein LlHB16 to attenuate basal thermotolerance in lily

Homeodomain-leucine zipper (HD-Zip) I transcription factors are crucial for plant responses to drought, salt, and cold stresses. However, how they are associated with thermotolerance remains mostly unknown. We previously demonstrated that lily (Lilium longiflorum) LlHB16 (HOMEOBOX PROTEIN 16) promotes thermotolerance, whereas the roles of other HD-Zip I members are still unclear. Here, we conducted a transcriptomic analysis and identified a heat-responsive HD-Zip I gene, LlHOX6 (HOMEOBOX 6). We showed that LlHOX6 represses the establishment of basal thermotolerance in lily. LlHOX6 expression was rapidly activated by high temperature, and its protein localized to the nucleus. Heterologous expression of LlHOX6 in Arabidopsis (Arabidopsis thaliana) and overexpression in lily reduced their basal thermotolerance. In contrast, silencing LlHOX6 in lily elevated basal thermotolerance. Cooverexpressing or cosilencing LlHOX6 and LlHB16 in vivo compromised their functions in modulating basal thermotolerance. LlHOX6 interacted with itself and with LlHB16, although heterologous interactions were stronger than homologous ones. Notably, LlHOX6 directly bounds DNA elements to repress the expression of the LlHB16 target genes LlHSFA2 (HEAT STRESS TRANSCRIPTION FACTOR A2) and LlMBF1c (MULTIPROTEIN BRIDGING FACTOR 1C). Moreover, LlHB16 activated itself to form a positive feedback loop, while LlHOX6 repressed LlHB16 expression. The LlHOX6-LlHB16 heterooligomers exhibited stronger DNA binding to compete for LlHB16 homooligomers, thus weakening the transactivation ability of LlHB16 for LlHSFA2 and LlMBF1c and reducing its autoactivation. Altogether, our findings demonstrate that LlHOX6 interacts with LlHB16 to limit its transactivation, thereby impairing heat stress responses in lily.

The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula

Legumes establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules. Nodules are modified lateral roots that undergo changes in their cellular development in response to bacteria, but the transcriptional reprogramming that occurs in these root cells remains largely uncharacterized. Here, we describe the cell-type-specific transcriptome response of Medicago truncatula roots to rhizobia during early nodule development in the wild-type genotype Jemalong A17, complemented with a hypernodulating mutant (sunn-4) to expand the cell population responding to infection and subsequent biological inferences. The analysis identifies epidermal root hair and stele sub-cell types associated with a symbiotic response to infection and regulation of nodule proliferation. Trajectory inference shows cortex-derived cell lineages differentiating to form the nodule primordia and, posteriorly, its meristem, while modulating the regulation of phytohormone-related genes. Gene regulatory analysis of the cell transcriptomes identifies new regulators of nodulation, including STYLISH 4, for which the function is validated.

The WOX Genes from the Intermediate Clade: Influence on the Somatic Embryogenesis in Medicago truncatula

Transcription factors from the WOX family are well-known regulators of cell proliferation and differentiation in plants. Herein, we focused on several WOX genes from the intermediate clade and checked their impact on somatic embryogenesis using the model legume object Medicago truncatula. As a result, we show that MtWOX9-1 overexpression not only stimulates somatic embryogenesis in the embryogenic M. truncatula line, as it was shown previously, but can also induce somatic embryogenesis in the non-embryogenic line. Other intermediate clade WOX, including the close paralog of MtWOX9-1, as well as WOX11 homologs, did not have any significant impact on somatic embryogenesis in our in vitro cultivation system. Together, our results give new information about the diversity of the WOX family proteins and their specific functions. These data can be used for the search of new regeneration stimulators.

MtWOX2 and MtWOX9-1 Effects on the Embryogenic Callus Transcriptome in Medicago truncatula

WOX family transcription factors are well-known regulators of plant development, controlling cell proliferation and differentiation in diverse organs and tissues. Several WOX genes have been shown to participate in regeneration processes which take place in plant cell cultures in vitro, but the effects of most of them on tissue culture development have not been discovered yet. In this study, we evaluated the effects of MtWOX2 gene overexpression on the embryogenic callus development and transcriptomic state in Medicago truncatula. According to our results, overexpression of MtWOX2 leads to an increase in callus weight. Furthermore, transcriptomic changes in MtWOX2 overexpressing calli are, to a large extent, opposite to the changes caused by overexpression of MtWOX9-1, a somatic embryogenesis stimulator. These results add new information about the mechanisms of interaction between different WOX genes and can be useful for the search of new regeneration regulators.

MdHB7-like positively modulates apple salt tolerance by promoting autophagic activity and Na+ efflux

Salt stress adversely affects the yield and quality of crops and limits their geographical distribution. Studying the functions and regulatory mechanisms of key genes in the salt stress response is important for breeding crops with enhanced stress resistance. Autophagy plays an important role in modulating the tolerance of plants to various types of abiotic stressors. However, the mechanisms underlying salt-induced autophagy are largely unknown. Cation/Ca2+ exchanger proteins enhance apple salt tolerance by inhibiting Na+ accumulation but the mechanism underlying the response to salt stress remains unclear. Here, we show that the autophagy-related gene MdATG18a modulated apple salt tolerance. Under salt stress, the autophagic activity, proline content, and antioxidant enzyme activities were higher and Na+ accumulation was lower in MdATG18a-overexpressing transgenic plants than in control plants. The use of an autophagy inhibitor during the salt treatment demonstrated that the regulatory function of MdATG18a depended on autophagy. The yeast-one-hybrid assay revealed that the homeodomain-leucine zipper (HD-Zip) transcription factor MdHB7-like directly bound to the MdATG18a promoter. Transcriptional regulation and genetic analyses showed that MdHB7-like enhanced salt-induced autophagic activity by promoting MdATG18a expression. The analysis of Na+ efflux rate in transgenic yeast indicated that MdCCX1 expression significantly promoted Na+ efflux. Promoter binding, transcriptional regulation, and genetic analyses showed that MdHB7-like promoted Na+ efflux and apple salt tolerance by directly promoting MdCCX1 expression, which was independent of the autophagy pathway. Overall, our findings provide insight into the mechanism underlying MdHB7-like-mediated salt tolerance in apple through the MdHB7-like-MdATG18a and MdHB7-like-MdCCX1 modules. These results will aid future studies on the mechanisms underlying stress-induced autophagy and the regulation of stress tolerance in plants.

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).

Genome-wide identification, bioinformatics and expression analysis of HD-Zip gene family in peach

BACKGROUND

HD-Zips (Homeodomain-Leucine Zippers) are a class of plant-specific transcription factors that play multiple roles in plant growth and development. Although some functions of HD-Zip transcription factor have been reported in several plants, it has not been comprehensively studied in peach, especially during adventitious root formation of peach cuttings.

RESULTS

In this study, 23 HD-Zip genes distributed on 6 chromosomes were identified from the peach (Prunus persica) genome, and named PpHDZ01-23 according to their positions on the chromosomes. These 23 PpHDZ transcription factors all contained a homeomorphism box domain and a leucine zipper domain, were divided into 4 subfamilies(I-IV) according to the evolutionary analysis, and their promoters contained many different cis-acting elements. Spatio-temporal expression pattern showed that these genes were expressed in many tissues with different levels, and they had distinct expression pattern during adventitious root formation and development.

CONCLUSION

Our results showed the roles of PpHDZs on root formation, which is helpful to better understand the classification and function of peach HD-Zip genes.

Temperature increase modifies susceptibility to Verticillium wilt in Medicago spp and may contribute to the emergence of more aggressive pathogenic strains

Global warming is expected to have a direct impact on plant disease patterns in agro-eco-systems. However, few analyses report the effect of moderate temperature increase on disease severity due to soil-borne pathogens. For legumes, modifications of root plant-microbe interactions either mutualistic or pathogenic due to climate change may have dramatic effects. We investigated the effect of increasing temperature on the quantitative disease resistance to Verticillium spp., a major soil-borne fungal pathogen, in the model legume Medicago truncatula and the crop M. sativa. First, twelve pathogenic strains isolated from various geographical origin were characterized with regard to their in vitro growth and pathogenicity at 20°C, 25°C and 28°C. Most of them exhibited 25°C as the optimum temperature for in vitro parameters, and between 20°C and 25°C for pathogenicity. Second, a V. alfalfae strain was adapted to the higher temperature by experimental evolution, i.e. three rounds of UV mutagenesis and selection for pathogenicity at 28°C on a susceptible M. truncatula genotype. Inoculation of monospore isolates of these mutants on resistant and susceptible M. truncatula accessions revealed that at 28°C they were all more aggressive than the wild type strain, and that some had acquired the ability to cause disease on resistant genotype. Third, one mutant strain was selected for further studies of the effect of temperature increase on the response of M. truncatula and M. sativa (cultivated alfalfa). The response of seven contrasted M. truncatula genotypes and three alfalfa varieties to root inoculation was followed using disease severity and plant colonization, at 20°C, 25°C and 28°C. With increasing temperature, some lines switched from resistant (no symptoms, no fungus in the tissues) to tolerant (no symptoms but fungal growth into the tissues) phenotypes, or from partially resistant to susceptible. Further studies in greenhouse evidence the reduction in plant fitness due to disease in susceptible lines. We thus report that root pathogenic interactions are affected by anticipated global warming, with trends towards increased plant susceptibility and larger virulence for hot-adapted strains. New threats due to hot-adapted strains of soil-borne pathogens, with possibly wider host range and increased aggressiveness, might occur.

Overexpression of Pyrus sinkiangensis HAT5 enhances drought and salt tolerance, and low-temperature sensitivity in transgenic tomato

The homeodomain-leucine zipper protein HAT belongs to the homeodomain leucine zipper subfamily (HD-Zip) and is important for regulating plant growth and development and stress tolerance. To investigate the role of HAT5 in tolerance to drought, salt, and low temperature stress, we selected a HAT gene from Pyrus sinkiangensis Yü (Pyrus sinkiangensis T.T. Yu). The sequences were analyzed using ioinformatics, and the overexpressed tomato lines were obtained using molecular biology techniques. The phenotypes, physiological, and biochemical indexes of the wild-type and transgenic tomato lines were observed under different stress conditions. We found that the gene had the highest homology with PbrHAT5. Under drought and NaCl stress, osmotic regulatory substances (especially proline) were significantly accumulated, and antioxidant enzyme activities were enhanced. The malondialdehyde level and relative electrical conductivity of transgenic tomatoes under low temperature (freezing) stress were significantly higher than those of wild-type tomatoes. The reactive oxygen species scavenging system was unbalanced. This study found that PsHAT5 improved the tolerance of tomatoes to drought and salt stress by regulating proline metabolism and oxidative stress ability, reducing the production of reactive oxygen species, and maintaining normal cell metabolism. In conclusion, the PsHAT5 transcription factor has great potential in crop resistance breeding, which lays a theoretical foundation for future excavation of effective resistance genes of the HD-Zip family and experimental field studies.

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.

The regulatory role of abscisic acid on cadmium uptake, accumulation and translocation in plants

To date, Cd contamination of cropland and crops is receiving more and more attention around the world. As a plant hormone, abscisic acid (ABA) plays an important role in Cd stress response, but its effect on plant Cd uptake and translocation varies among plant species. In some species, such as Arabidopsis thaliana, Oryza sativa, Brassica chinensis, Populus euphratica, Lactuca sativa, and Solanum lycopersicum, ABA inhibits Cd uptake and translocation, while in other species, such as Solanum photeinocarpum and Boehmeria nivea, ABA severs the opposite effect. Interestingly, differences in the methods and concentrations of ABA addition also triggered the opposite result of Cd uptake and translocation in Sedum alfredii. The regulatory mechanism of ABA involved in Cd uptake and accumulation in plants is still not well-established. Therefore, we summarized the latest studies on the ABA synthesis pathway and comparatively analyzed the physiological and molecular mechanisms related to ABA uptake, translocation, and detoxification of Cd in plants at different ABA concentrations or among different species. We believe that the control of Cd uptake and accumulation in plant tissues can be achieved by the appropriate ABA application methods and concentrations in plants.

Tolerant mechanism of model legume plant Medicago truncatula to drought, salt, and cold stresses

Legume plants produce one-third of the total yield of primary crops and are important food sources for both humans and animals worldwide. Frequent exposure to abiotic stresses, such as drought, salt, and cold, greatly limits the production of legume crops. Several morphological, physiological, and molecular studies have been conducted to characterize the response and adaptation mechanism to abiotic stresses. The tolerant mechanisms of the model legume plant Medicago truncatula to abiotic stresses have been extensively studied. Although many potential genes and integrated networks underlying the M. truncatula in responding to abiotic stresses have been identified and described, a comprehensive summary of the tolerant mechanism is lacking. In this review, we provide a comprehensive summary of the adaptive mechanism by which M. truncatula responds to drought, salt, and cold stress. We also discuss future research that need to be explored to improve the abiotic tolerance of legume plants.

Overexpression of McHB7 Transcription Factor from Mesembryanthemum crystallinum Improves Plant Salt Tolerance

Mesembryanthemum crystallinum (common ice plant) is one of the facultative halophyte plants, and it serves as a model for investigating the molecular mechanisms underlying its salt stress response and tolerance. Here we cloned one of the homeobox transcription factor (TF) genes, McHB7, from the ice plant, which has 60% similarity with the Arabidopsis AtHB7. Overexpression of the McHB7 in Arabidopsis (OE) showed that the plants had significantly elevated relative water content (RWC), chlorophyll content, superoxide dismutase (SOD), and peroxidase (POD) activities after salt stress treatment. Our proteomic analysis identified 145 proteins to be significantly changed in abundance, and 66 were exclusively increased in the OE plants compared to the wild type (WT). After salt treatment, 979 and 959 metabolites were significantly increased and decreased, respectively, in the OE plants compared to the WT. The results demonstrate that the McHB7 can improve photosynthesis, increase the leaf chlorophyll content, and affect the TCA cycle by regulating metabolites (e.g., pyruvate) and proteins (e.g., citrate synthase). Moreover, McHB7 modulates the expression of stress-related proteins (e.g., superoxide dismutase, dehydroascorbate reductase, and pyrroline-5-carboxylate synthase B) to scavenge reactive oxygen species and enhance plant salt tolerance.

At the Crossroads of Salinity and Rhizobium-Legume Symbiosis

Legume roots interact with soil bacteria rhizobia to develop nodules, de novo symbiotic root organs that host these rhizobia and are mini factories of atmospheric nitrogen fixation. Nodulation is a sophisticated developmental process and is sensitive to several abiotic factors, salinity being one of them. While salinity influences both the free-living partners, symbiosis is more vulnerable than other aspects of plant and microbe physiology, and the symbiotic interaction is strongly impaired even under moderate salinity. In this review, we tease apart the various known components of rhizobium-legume symbiosis and how they interact with salt stress. We focus primarily on the initial stages of symbiosis since we have a greater mechanistic understanding of the interaction at these stages.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

ZmLBD5 Increases Drought Sensitivity by Suppressing ROS Accumulation in Arabidopsis

Drought stress is known to significantly limit crop growth and productivity. Lateral organ boundary domain (LBD) transcription factors-particularly class-I members-play essential roles in plant development and biotic stress. However, little information is available on class-II LBD genes related to abiotic stress in maize. Here, we cloned a maize class-II LBD transcription factor, ZmLBD5, and identified its function in drought stress. Transient expression, transactivation, and dimerization assays demonstrated that ZmLBD5 was localized in the nucleus, without transactivation, and could form a homodimer or heterodimer. Promoter analysis demonstrated that multiple drought-stress-related and ABA response cis-acting elements are present in the promoter region of ZmLBD5. Overexpression of ZmLBD5 in Arabidopsis promotes plant growth under normal conditions, and suppresses drought tolerance under drought conditions. Furthermore, the overexpression of ZmLBD5 increased the water loss rate, stomatal number, and stomatal apertures. DAB and NBT staining demonstrated that the reactive oxygen species (ROS) decreased in ZmLBD5-overexpressed Arabidopsis. A physiological index assay also revealed that SOD and POD activities in ZmLBD5-overexpressed Arabidopsis were higher than those in wild-type Arabidopsis. These results revealed the role of ZmLBD5 in drought stress by regulating ROS levels.

Identification and characterization of stress responsive homeodomain leucine zipper transcription factors in Medicago truncatula

BACKGROUND

Homeodomain leucine zipper (HD-ZIP) transcription factors play roles in regulating plant development and responses to abiotic stresses; however, how HD-ZIP genes in Medicago truncatula are involved in abiotic stress response remains elusive.

METHODS AND RESULTS

The HD-ZIP I genes in Medicago truncatula were identified and characterized, and their expression patterns in different tissues and under different abiotic stresses were analyzed. A total of 15 Medicago truncatula HD-ZIP I genes were identified and a phylogenetic analysis of HD-ZIP I proteins in Arabidopsis thaliana and Medicago truncatula was conducted. Fifteen HD-ZIP I genes showed diverse tissue preferences. Among them, expressions of MtHB22 and MtHB51 were specially detected in vegetative buds. In addition, they responded to various abiotic stresses, including salinity and osmotic stress and abscisic acid (ABA). For instance, MtHB7 and MtHB12 expression levels were found to be positively associated with salt, osmotic stress and ABA in both shoots and roots, while MtHB13 and MtHB23 were negatively associated with these stresses in Medicago truncatula.

CONCLUSION

The HD-ZIP I genes in Medicago truncatula are evolutionarily conserved, but also exhibit gene duplication and gene loss events. Differential expression analysis of Medicago truncatula HD-ZIP I genes indicated their crucial roles in abiotic stress responses. Our genome-wide analysis of the HD-ZIP I transcription factor family in Medicago truncatula provided a valuable reference for further research.

Genome-Wide Analysis of KNOX Transcription Factors and Expression Pattern of Dwarf-Related KNOX Genes in Pear

KNOTTED1-like homeobox (KNOX) transcription factors (TFs) belonging to the homeobox TF family play important roles in plant growth, development, and responses to abiotic and biotic stress. However, little information is available on KNOX TF in pear (Pyrus). In this study, 19 PbKNOXs TFs were re-identified in pear (Pyrus bretschneideri Rehd.). Phylogenetic analysis revealed that the TFs were clustered into three groups with 10 conserved motifs, some of which were group- or subgroup-specific, implying that they are important for the functions of the KNOX in these clades. PbKNM1 and PbKNM2 are KNM (encodes a MEINOX domain but not a homeodomain) genes identified in pear for the first time. KNOX genes in Pyrus and Malus were closely related, and a collinear relationship among PbKNOX genes in Pyrus and Malus was observed. Analysis of the expression patterns of PbKNOX genes in different tissues, at various growth stages, and in response to abiotic and biotic stress revealed that PbKNOXs are involved in plant growth and development. Our comparative transcriptional analysis of dwarf mutant varieties revealed that genes belonging to class I are highly expressed compared with genes in other classes. Analysis of the expression of PbKNOX genes in the hybrid offspring of vigorous and dwarf varieties revealed that PbKNOX genes were highly expressed in the vigorous offspring and weakly expressed in the dwarf offspring. These findings provide new insight into the function of KNOX TFs in pear and will aid future studies of dwarf fruit trees.

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.

Overexpression of the CaHB12 transcription factor in cotton (Gossypium hirsutum) improves drought tolerance

The Coffea arabica HB12 gene (CaHB12), which encodes a transcription factor belonging to the HD-Zip I subfamily, is upregulated under drought, and its constitutive overexpression (35S:CaHB12^OX) improves the Arabidopsis thaliana tolerance to drought and salinity stresses. Herein, we generated transgenic cotton events constitutively overexpressing the CaHB12 gene, characterized these events based on their increased tolerance to water deficit, and exploited the gene expression level from the CaHB12 network. The segregating events Ev8.29.1, Ev8.90.1, and Ev23.36.1 showed higher photosynthetic yield and higher water use efficiency under severe water deficit and permanent wilting point conditions compared to wild-type plants. Under well-irrigated conditions, these three promising transformed events showed an equivalent level of Abscisic acid (ABA) and decreased Indole-3-acetic acid (IAA) accumulation, and a higher putrescine/(spermidine + spermine) ratio in leaf tissues was found in the progenies of at least two transgenic cotton events compared to non-transgenic plants. In addition, genes that are considered as modulated in the A. thaliana 35S:CaHB12^OX line were also shown to be modulated in several transgenic cotton events maintained under field capacity conditions. The upregulation of GhPP2C and GhSnRK2 in transgenic cotton events maintained under permanent wilting point conditions suggested that CaHB12 might act enhancing the ABA-dependent pathway. All these data confirmed that CaHB12 overexpression improved the tolerance to water deficit, and the transcriptional modulation of genes related to the ABA signaling pathway or downstream genes might enhance the defense responses to drought. The observed decrease in IAA levels indicates that CaHB12 overexpression can prevent leaf abscission in plants under or after stress. Thus, our findings provide new insights on CaHB12 gene and identify several promising cotton events for conducting field trials on water deficit tolerance and agronomic performance.

Salt Stress Enhances Early Symbiotic Gene Expression in Medicago truncatula and Induces a Stress-Specific Set of Rhizobium-Responsive Genes

Salt stress is a major agricultural concern inhibiting not only plant growth but also the symbiotic association between legume roots and the soil bacteria rhizobia. This symbiotic association is initiated by a molecular dialogue between the two partners, leading to the activation of a signaling cascade in the legume host and, ultimately, the formation of nitrogen-fixing root nodules. Here, we show that a moderate salt stress increases the responsiveness of early symbiotic genes in Medicago truncatula to its symbiotic partner, Sinorhizobium meliloti while, conversely, inoculation with S. meliloti counteracts salt-regulated gene expression, restoring one-third to control levels. Our analysis of early nodulin 11 (ENOD11) shows that salt-induced expression is dynamic, Nod-factor dependent, and requires the ionic but not the osmotic component of salt. We demonstrate that salt stimulation of rhizobium-induced gene expression requires NSP2, which functions as a node to integrate the abiotic and biotic signals. In addition, our work reveals that inoculation with S. meliloti succinoglycan mutants also hyperinduces ENOD11 expression in the presence or absence of salt, suggesting a possible link between rhizobial exopolysaccharide and the plant response to salt stress. Finally, we identify an accessory set of genes that are induced by rhizobium only under conditions of salt stress and have not been previously identified as being nodulation-related genes. Our data suggest that interplay of core nodulation genes with different accessory sets, specific for different abiotic conditions, functions to establish the symbiosis. Together, our findings reveal a complex and dynamic interaction between plant, microbe, and environment.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

The HD-Zip I transcription factor MdHB7-like confers tolerance to salinity in transgenic apple (Malus domestica)

Salinity is a major environmental constraint that substantially limits global agricultural productivity. HD-Zip I transcription factors are involved in plant responses to salt stress, but little is known about the HD-Zip I genes in apple (Malus domestica). Here, we characterized the function of an apple HD-Zip I gene (MdHB7-like) and report that its expression is induced by salt stress. To further explore its role in salt stress, we created MdHB7-like overexpressing and RNAi transgenic apple plants. The overexpression of MdHB7-like improved the photosynthetic performance and reduced ROS and Na⁺ accumulation under salt stress. Plants that overexpressed MdHB7-like also showed increased accumulation of proline and soluble sugars, which may have played an important role in their salt stress tolerance. RNAi suppression of MdHB7-like had the opposite effects. Together, our results demonstrate that MdHB7-like is an important regulator of salt tolerance in apple. Our results provide new insights for future research on the mechanisms by which MdHB7-like promotes salt tolerance and provide a potential target for molecular breeding in apple.

Root-omics for drought tolerance in cool-season grain legumes

Root traits can be exploited to increase the physiological efficiency of crop water use under drought. Root length, root hairs, root branching, root diameter, and root proliferation rate are genetically defined traits that can help to improve the water productivity potential of crops. Recently, high-throughput phenotyping techniques/platforms have been used to screen the germplasm of major cool-season grain legumes for root traits and their impact on different physiological processes, including nutrient uptake and yield potential. Advances in omics approaches have led to the dissection of genomic, proteomic, and metabolomic structures of these traits. This knowledge facilitates breeders to improve the water productivity and nutrient uptake of cultivars under limited soil moisture conditions in major cool-season grain legumes that usually face terminal drought. This review discusses the advances in root traits and their potential for developing drought-tolerant cultivars in cool-season grain legumes.

The underground life of homeodomain-leucine zipper transcription factors

Roots are the anchorage organs of plants, responsible for water and nutrient uptake, exhibiting high plasticity. Root architecture is driven by the interactions of biomolecules, including transcription factors and hormones that are crucial players regulating root plasticity. Multiple transcription factor families are involved in root development; some, such as ARFs and LBDs, have been well characterized, whereas others remain less well investigated. In this review, we synthesize the current knowledge about the involvement of the large family of homeodomain-leucine zipper (HD-Zip) transcription factors in root development. This family is divided into four subfamilies (I-IV), mainly according to structural features, such as additional motifs aside from HD-Zip, as well as their size, gene structure, and expression patterns. We explored and analyzed public databases and the scientific literature regarding HD-Zip transcription factors in Arabidopsis and other species. Most members of the four HD-Zip subfamilies are expressed in specific cell types and several individuals from each group have assigned functions in root development. Notably, a high proportion of the studied proteins are part of intricate regulation pathways involved in primary and lateral root growth and development.

Auxin Response Factor 2 (ARF2), ARF3, and ARF4 Mediate Both Lateral Root and Nitrogen Fixing Nodule Development in Medicago truncatula

Auxin Response Factors (ARFs) constitute a large family of transcription factors that mediate auxin-regulated developmental programs in plants. ARF2, ARF3, and ARF4 are post-transcriptionally regulated by the microRNA390 (miR390)/trans-acting small interference RNA 3 (TAS3) module through the action of TAS3-derived trans - acting small interfering RNAs (ta-siRNA). We have previously reported that constitutive activation of the miR390/TAS3 pathway promotes elongation of lateral roots but impairs nodule organogenesis and infection by rhizobia during the nitrogen-fixing symbiosis established between Medicago truncatula and its partner Sinorhizobium meliloti. However, the involvement of the targets of the miR390/TAS3 pathway, i.e., MtARF2, MtARF3, MtARF4a, and MtARF4b, in root development and establishment of the nitrogen-fixing symbiosis remained unexplored. Here, promoter:reporter fusions showed that expression of both MtARF3 and MtARF4a was associated with lateral root development; however, only the MtARF4a promoter was active in developing nodules. In addition, up-regulation of MtARF2, MtARF3, and MtARF4a/b in response to rhizobia depends on Nod Factor perception. We provide evidence that simultaneous knockdown of MtARF2, MtARF3, MtARF4a, and MtARF4b or mutation in MtARF4a impaired nodule formation, and reduced initiation and progression of infection events. Silencing of MtARF2, MtARF3, MtARF4a, and MtARF4b altered mRNA levels of the early nodulation gene nodulation signaling pathway 2 (MtNSP2). In addition, roots with reduced levels of MtARF2, MtARF3, MtARF4a, and MtARF4b, as well as arf4a mutant plants exhibited altered root architecture, causing a reduction in primary and lateral root length, but increasing lateral root density. Taken together, our results suggest that these ARF members are common key players of the morphogenetic programs that control root development and the formation of nitrogen-fixing nodules.

A moso bamboo transcription factor, Phehdz1, positively regulates the drought stress response of transgenic rice

78 HD-Zip family genes in Phyllostachys edulis were analyzed. Overexpression of Phehdz1 can improve the drought tolerance of transgenic rice and affect its secondary metabolism. Many studies suggested homeodomain-leucine zipper (HD-Zip) transcription factors are important regulators of plant growth and development, signal transduction, and responses to environmental stresses. In this study, 78 moso bamboo (Phyllostachys edulis) HD-Zip genes were investigated and classified into four subfamilies (HD-Zip I-IV). Additionally, Phehdz1 (HD-Zip I gene) was isolated and confirmed to be highly expressed in the roots. A quantitative real-time PCR analysis indicated Phehdz1 expression was significantly induced by drought, high salinity, and abscisic acid (ABA). A transient expression assay proved that Phehdz1 was localized in the nucleus of tobacco cells. Moreover, it could bind to the core region encoded by the H-box sequence (CAATAATTG) in yeast. In response to mannitol treatments, the Phehdz1-overexpressing transgenic rice had a higher germination rate and longer shoots than the wild-type controls. Moreover, Phehdz1-overexpressing rice plants had a higher survival rate as well as higher relative water and proline contents, but a lower malondialdehyde content, than the WT plants after a 30% polyethylene glycol 6000 treatment. Accordingly, the overexpression of Phehdz1 enhances the drought tolerance of transgenic rice. Many of the differentially expressed genes identified by a transcriptome analysis are involved in MAPK signal transduction and the biosynthesis of secondary metabolites. Thus, the overexpression of Phehdz1 enhances the drought stress tolerance of transgenic rice, while also potentially modulating the expression of metabolism-related genes.

CRISPR/Cas9 targeted mutagenesis of SlLBD40, a lateral organ boundaries domain transcription factor, enhances drought tolerance in tomato

The LATERAL ORGAN BOUNDARIES DOMAIN (LBD)-containing genes are plant-specific genes that play important roles in lateral organ development. In this study, we identified LBD40 (Solyc02g085910), which belongs to subfamily II of the LBD family of genes in tomato. LBD40 was highly expressed in roots and fruit. LBD40 expression was significantly induced by PEG and salt. Moreover, SlLBD40 expression was induced by methyl jasmonate treatment, while SlLBD40 expression could not be induced in the jasmonic acid-insensitive1 (jai1) mutant or MYC2-silenced plants, in which jasmonic acid (JA) signaling was disrupted. These findings demonstrate that SlLBD40 expression was dependent on JA signaling and that it might be downstream of SlMYC2, which is the master transcription factor in the JA signal transduction pathway. Overexpressing and CRISPR/Cas9 mediated knockout transgenic tomato plants were generated to explore SlLBD40 function. The drought tolerance test showed that two SlLBD40 knockout lines wilted slightly, while SlLBD40 overexpressing plants suffered severe wilting. The statistical water loss rate and midday leaf water potential also confirmed that knockout of SlLBD40 improved the water-holding ability of tomato under drought conditions. Taken together, our study demonstrates that SlLBD40, involved in JA signaling, was a negative regulator of drought tolerance and that knockout of SlLBD40 enhanced drought tolerance in tomato. This study also provides a novel function of SlLBD40, which belongs to subfamily II of LBD genes.

PuHox52-mediated hierarchical multilayered gene regulatory network promotes adventitious root formation in Populus ussuriensis

Adventitious root (AR) formation is critically important in vegetative propagation through cuttings in some plants, especially woody species. However, the underlying molecular mechanisms remain elusive. Here, we report the identification of a poplar homeobox gene, PuHox52, which was induced rapidly (within 15 min) at the basal ends of stems upon cutting and played a key regulatory role in adventitious rooting. We demonstrated that overexpression of PuHox52 significantly increased the number of ARs while suppression of PuHox52 had the opposite effect. A multilayered hierarchical gene regulatory network (ML-hGRN) mediated by PuHox52 was reverse-engineered and demonstrated to govern AR formation. PuHox52 regulated AR formation through upregulation of nine hub regulators, including a jasmonate signaling pathway gene, PuMYC2, and an auxin signaling pathway gene, PuAGL12. We also identified coherent type 4 feed-forward loops within this ML-hGRN; PuHox52 repressed PuHDA9, which encodes a histone deacetylase, and led to an increase in acetylation and presumably expression of three hub regulators, PuWRKY51, PuLBD21 and PuIAA7. Our results indicate that the ML-hGRN mediated by PuHox52 governs AR formation at the basal ends of stem cuttings from poplar trees.

HvHOX9, a novel homeobox leucine zipper transcription factor, positively regulates aluminum tolerance in Tibetan wild barley

Aluminum (Al) toxicity is the primary limiting factor of crop production on acid soils. Tibetan wild barley germplasm is a valuable source of potential genes for breeding barley with acid and Al tolerance. We performed microRNA and RNA sequencing using wild (XZ16, Al-tolerant; XZ61, Al-sensitive) and cultivated (Dayton, Al-tolerant) barley. A novel homeobox-leucine zipper transcription factor, HvHOX9, was identified as a target gene of miR166b and functionally characterized. HvHOX9 was up-regulated by Al stress in XZ16 (but unchanged in XZ61 and Dayton) and was significantly induced only in root tip. Phylogenetic analysis showed that HvHOX9 is most closely related to wheat TaHOX9 and orthologues of HvHOX9 are present in the closest algal relatives of Zygnematophyceae. Barley stripe mosaic virus-induced gene silencing of HvHOX9 in XZ16 led to significantly increased Al sensitivity but did not affect its sensitivity to other metals and low pH. Disruption of HvHOX9 did not change Al concentration in the root cell sap, but led to more Al accumulation in root cell wall after Al exposure. Silencing of HvHOX9 decreased H+ influx after Al exposure. Our findings suggest that miR166b/HvHOX9 play a critical role in Al tolerance by decreasing root cell wall Al binding and increasing apoplastic pH for Al detoxification in the root.

Genome-wide characterization and expression profiling of Eucalyptus grandis HD-Zip gene family in response to salt and temperature stress

BACKGROUND

The HD-Zip transcription factors are unique to plants and play an essential role in plant growth, development and stress responses. The HD-Zip transcription factor family consists of a highly conserved homeodomain (HD) and a leucine zipper domain (LZ) domain. Although the HD-Zip gene family has been extensively studied in many plant species, a systematic study of the Eucalyptus HD-Zip family has not been reported until today. Here, we systematically identified 40 HD-Zip genes in Eucalyptus (Eucalyptus grandis). Besides, we comprehensively analyzed the HD-Zips of Eucalyptus by studying the homology, conserved protein regions, gene structure, 3D structure of the protein, location of the genes on the chromosomes and the expression level of the genes in different tissues.

RESULTS

The HD-Zip family in Eucalyptus has four subfamilies, which is consistent with other plants such as Arabidopsis and rice. Moreover, genes that are in the same group tend to have similar exon-intron structures, motifs, and protein structures. Under salt stress and temperature stress, the Eucalyptus HD-Zip transcription factors show a differential expression pattern.

CONCLUSIONS

Our findings reveal the response of HD-Zip transcription factors under salt and temperature stresses, laying a foundation for future analysis of Eucalyptus HD-Zip transcription factors.

AtHB7/12 Regulate Root Growth in Response to Aluminum Stress

Aluminum (Al) stress is a major limiting factor for plant growth and crop production in acid soils. At present, only a few transcription factors involved in the regulation of Al resistance have been characterized. Here, we used reversed genetic approach through phenotype analysis of overexpressors and mutants to demonstrate that AtHB7 and AtHB12, two HD-Zip I transcription factors, participate in Al resistance. In response to Al stress, AtHB7 and AtHB12 displayed different dynamic expression patterns. Although both AtHB7 and AtHB12 positively regulate root growth in the absence of Al stress, our results showed that AtHB7 antagonizes with AtHB12 to control root growth in response to Al stress. The athb7/12 double mutant displayed a wild-type phenotype under Al stress. Consistently, our physiological analysis showed that AtHB7 and AtHB12 oppositely regulate the capacity of cell wall to bind Al. Yeast two hybrid assays showed that AtHB7 and AtHB12 could form homo-dimers and hetero-dimers in vitro, suggesting the interaction between AtHB7 and AtHB12 in the regulation of root growth. The conclusion was that AtHB7 and AtHB12 oppositely regulate Al resistance by affecting Al accumulation in root cell wall.

The RhHB1/RhLOX4 module affects the dehydration tolerance of rose flowers (Rosa hybrida) by fine-tuning jasmonic acid levels

Phytohormones are key factors in plant responsiveness to abiotic and biotic stresses, and maintaining hormone homeostasis is critically important during stress responses. Cut rose (Rosa hybrida) flowers experience dehydration stress during postharvest handling, and jasmonic acid (JA) levels change as a result of this stress. However, how JA is involved in dehydration tolerance remains unclear. We investigated the functions of the JA- and dehydration-induced RhHB1 gene, which encodes a homeodomain-leucine zipper I γ-clade transcription factor, in rose flowers. Silencing RhHB1 decreased petal dehydration tolerance and resulted in a persistent increase in JA-Ile content and reduced dehydration tolerance. An elevated JA-Ile level had a detrimental effect on rose petal dehydration tolerance. RhHB1 was shown to lower the transient induction of JA-Ile accumulation in response to dehydration. In addition to transcriptomic data, we obtained evidence that RhHB1 suppresses the expression of the lipoxygenase 4 (RhLOX4) gene by directly binding to its promoter both in vivo and in vitro. We propose that increased JA-Ile levels weaken the capacity for osmotic adjustment in petal cells, resulting in reduced dehydration tolerance. In conclusion, a JA feedback loop mediated by an RhHB1/RhLOX4 regulatory module provides dehydration tolerance by fine-tuning bioactive JA levels in dehydrated flowers.

Phylogeny and Functions of LOB Domain Proteins in Plants

Lateral organ boundaries (LOB) domain (LBD) genes, a gene family encoding plant-specific transcription factors, play important roles in plant growth and development. At present, though there have been a number of genome-wide analyses on LBD gene families and functional studies on individual LBD proteins, the diverse functions of LBD family members still confuse researchers and an effective strategy is required to summarize their functional diversity. To further integrate and improve our understanding of the phylogenetic classification, functional characteristics and regulatory mechanisms of LBD proteins, we review and discuss the functional characteristics of LBD proteins according to their classifications under a phylogenetic framework. It is proved that this strategy is effective in the anatomy of diverse functions of LBD family members. Additionally, by phylogenetic analysis, one monocot-specific and one eudicot-specific subclade of LBD proteins were found and their biological significance in monocot and eudicot development were also discussed separately. The review will help us better understand the functional diversity of LBD proteins and facilitate further studies on this plant-specific transcription factor family.

Genome-wide identification and expression profiling of HD-ZIP gene family in Medicago truncatula

The homeodomain-leucine zipper (HD-ZIP) transcription factors are important regulators in various developmental processes and responses to environmental stimuli. Currently, little information is available for HD-ZIP gene family in Medicago truncatula. Here we perform a genome-wide analysis of HD-ZIP gene family in M. truncatula. Totally 52 M. truncatula HD-ZIPs (MtHDZs) were identified and classified into four distinctive subfamilies (I to IV). Members clustered in the same subfamily shared similar gene structure and protein motifs. Fifty-one MtHDZs were non-evenly distributed on eight chromosomes. Segmental duplication and purifying selection mainly contributed to the expansion and retention of M. truncatula HD-ZIP gene family. Expression profiling using the publicly available microarray data revealed that MtHDZ genes exhibited distinctive tissue-specific patterns and divergent responses to drought and salt stresses. In addition, the expression profile between each paralogous pair diverged differentially. Our results identified potential targets for the genetic improvement of abiotic stress tolerance in Medicago.

Four HD-ZIPs are involved in banana fruit ripening by activating the transcription of ethylene biosynthetic and cell wall-modifying genes

Four MaHDZs are possibly involved in banana fruit ripening by activating the transcription of genes related to ethylene biosynthesis and cell wall degradation, such as MaACO5, MaEXP2, MaEXPA10, MaPG4 and MaPL4. The homeodomain-leucine zipper (HD-ZIP) proteins represent plant-specific transcription factors, which contribute to various plant physiological processes. However, little information is available regarding the association of HD-ZIPs with banana fruit ripening. In this study, we identified a total of 96 HD-ZIP genes in banana genome, which were divided into four different groups consisting of 35, 31, 9 and 21 members in the I, II, III and IV subfamilies, respectively. The expression patterns of MaHDZ genes during fruit ripening showed that MaHDZI.19, MaHDZI.26, MaHDZII.4 and MaHDZII.7 were significantly up-regulated in the ripening stage and thus suggested to be potential regulators of banana fruit ripening. Furthermore, MaHDZI.19, MaHDZI.26, MaHDZII.4 and MaHDZII.7 were found to localize exclusively in the nucleus and exhibit transcriptional activation capacities. Importantly, MaHDZI.19, MaHDZI.26, MaHDZII.4 and MaHDZII.7 stimulated the transcription of several ripening-related genes including MaACO5 related to ethylene biosynthesis, MaEXP2, MaEXPA10, MaPG4 and MaPL4 were associated with cell wall degradation, through directly binding to their promoters. Taken together, our findings expand the functions of HD-ZIP transcription factors and identify four MaHDZs likely involved in regulating banana fruit ripening by activating the expression of genes related to ethylene biosynthesis and cell wall modification, which may have potential application in banana molecular breeding.

The AtHB1 Transcription Factor Controls the miR164-CUC2 Regulatory Node to Modulate Leaf Development

The presence of small tooth-like indentations, or serrations, characterizes leaf margins of Arabidopsis thaliana plants. The NAC family member CUP-SHAPED COTYLEDON 2 (CUC2), which undergoes post-transcriptional gene silencing by three micro-RNA genes (MIR164A, B and C), controls the extension of leaf serration. Here, we analyzed the role of AtHB1, a transcription factor (TF) belonging to the homeodomain-leucine zipper subfamily I, in shaping leaf margins. Using mutants with an impaired silencing pathway as background, we obtained transgenic plants expressing AtHB1 over 100 times compared to controls. These plants presented an atypical developmental phenotype characterized by leaves with deep serration. Transcript measurements revealed that CUC2 expression was induced in plants overexpressing AtHB1 and repressed in athb1 mutants, indicating a positive regulation exerted by this TF. Moreover, molecular analyses of AtHB1 overexpressing and mutant plants revealed that AtHB1 represses MIR164 transcription. We found that overexpression of MIR164B was able to reverse the serration phenotype of plants overexpressing AtHB1. Finally, chromatin immunoprecipitation assays revealed that AtHB1 was able to bind in vivo the promoter regions of all three MIR164 encoding loci. Altogether, our results indicate that AtHB1 directly represses MIR164 expression to enhance leaf serration by increasing CUC2 levels.

Methane-induced lateral root formation requires the participation of nitric oxide signaling

Although methane (CH₄)-induced lateral root (LR) formation has been discovered, the identification of downstream signaling compounds has yet to be fully elucidated. Here, we report a unique mechanism for the involvement of nitric oxide (NO) in the above CH₄-mediated pathway in tomato (Solanum lycopersicum L.) and Arabidopsis thaliana. NO was produced rapidly in the root tissues of tomato seedlings when CH₄ was administrated exogenously. The scavenging of NO with its scavengers prevented lateral root primordia formation and thereafter lateral rooting triggered by CH₄. Gene expression analysis revealed that similar to the responses of sodium nitroprusside (SNP; a NO-releasing compound), CH₄-induced SlCYCA2;1, SlCYCA3;1, and SlCDKA1 transcripts, and -downregulated SlKRP2 mRNA, were differentially abolished when endogenous NO was removed by its scavengers. Changes in the lateral root-related miRNA genes (SlmiR160 and SlmiR390a) and their target genes (SlARF16 and SlARF4), exhibited similar tendencies. Similar to those results in tomato, the addition of CH₄ and SNP could obviously induce NO production and LR formation in Arabidopsis seedlings, which were correlated with the transcriptional profiles of representative LR-related genes. Combine with these findings in tomato and Arabidopsis thaliana, our results showed that NO might act, at least partially, as the downstream signaling molecule for CH₄ control of lateral rooting.

AtHB23 participates in the gene regulatory network controlling root branching, and reveals differences between secondary and tertiary roots

In Arabidopsis, lateral root (LR) development is mainly controlled by several known auxin-regulated transcription factors (TFs). Here, we show that AtHB23 (a homeodomain-leucine zipper I TF) participates in this intricate network. Our study of the expression pattern of AtHB23 revealed that it is transcriptionally activated in the early stages of secondary LR primordium (LRP). We found that AtHB23 directly limits the expression of LBD16, a key factor in LR initiation, and also directly induces the auxin transporter gene LAX3. We propose that this HD-Zip I mediates the regulation of LAX3 by ARF7/19. Furthermore, AtHB23 plays distinct roles during the formation of secondary and tertiary roots, exhibiting differential expression patterns. ATHB23 is expressed throughout the tertiary root primordium, whereas it is restricted to early stages in secondary primordia, likely later repressing LBD16 in tertiary LR development and further inhibiting root emergence. Our results suggest that different genetic programs govern the formation of LRP from the main or secondary roots, thereby shaping the global dynamic architecture of the root system.

The role of HD-Zip class I transcription factors in plant response to abiotic stresses

Abiotic stresses usually affect plant growth and development, indirectly or directly causing crop production reduction and even plant death. To survive, plants utilize different mechanisms to adapt themselves to continuously changing surrounding environmental stresses. Homeodomain-leucine zipper (HD-Zip) transcription factors are unique to the plant kingdom and divided into four different subfamilies (HD-Zip I∼IV). Many HD-Zip I members have been shown to play critical roles in the regulation of plant developmental processes, signaling networks and responses to environmental stresses. This review focuses on the role of HD-Zip I transcription factors in plant responses to various abiotic stresses, including abscisic acid-mediated stress, drought and cold stress, oxidative stress, helping to identify the potential regulatory mechanisms that alleviate abiotic stress in plants.

Genome-wide characterization and expression analysis of the HD-Zip gene family in response to drought and salinity stresses in sesame

Background

The homeodomain-leucine zipper (HD-Zip) gene family is one of the plant-specific transcription factor families, involved in plant development, growth, and in the response to diverse stresses. However, comprehensive analysis of the HD-Zip genes, especially those involved in response to drought and salinity stresses is lacking in sesame (Sesamum indicum L.), an important oil crop in tropical and subtropical areas.

Results

In this study, 45 HD-Zip genes were identified in sesame, and denominated as SiHDZ01-SiHDZ45. Members of SiHDZ family were classified into four groups (HD-Zip I-IV) based on the phylogenetic relationship of Arabidopsis HD-Zip proteins, which was further supported by the analysis of their conserved motifs and gene structures. Expression analyses of SiHDZ genes based on transcriptome data showed that the expression patterns of these genes were varied in different tissues. Additionally, we showed that at least 75% of the SiHDZ genes were differentially expressed in responses to drought and salinity treatments, and highlighted the important role of HD-Zip I and II genes in stress responses in sesame.

Conclusions

This study provides important information for functional characterization of stress-responsive HD-Zip genes and may contribute to the better understanding of the molecular basis of stress tolerance in sesame.

The HD-Zip transcription factor LcHB2 regulates litchi fruit abscission through the activation of two cellulase genes

Cellulases play important roles in the shedding of plant organs; however, little is yet known about the functions of cellulase genes during the process of organ abscission. Abnormal fruitlet abscission is a serious problem in the production of litchi (Litchi chinensis), an economically important fruit widely grown in South Asia. In this study, two abscission-accelerating treatments (carbohydrate stress and application of ethephon) were evaluated in litchi fruitlets. Cell wall degradation and cell separation were clearly observed in the abscission zones of treated fruitlets, consistent with enhanced cellulase activities and reduced cellulose contents. The expression of two cellulase genes (LcCEL2 and LcCEL8) was strongly associated with abscission. Floral organs of transgenic Arabidopsis overexpressing LcCEL2 or LcCEL8 showed remarkably precocious abscission. Electrophoretic mobility shift assays and transient expression experiments demonstrated that a novel homeodomain-leucine zipper transcription factor, LcHB2, could directly bind to and activate HD-binding cis-elements in the LcCEL2 and LcCEL8 promoters. Our results provide new information regarding the transcriptional regulation of the cellulase genes responsible for cell wall degradation and cell separation during plant organ shedding, and raise the possibility of future manipulation of litchi fruitlet abscission by modulation of the activities of these two cellulases.

Characterization and functional analysis of two novel 3-hydroxy-3-methylglutaryl-coenzyme A reductase genes (GbHMGR2 and GbHMGR3) from Ginkgo biloba

Terpene trilactones (TTLs) are the main secondary metabolites of Ginkgo biloba. As one of the rate-limiting enzymes in the mevalonic acid (MVA) pathway of TTL biosynthesis, 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR) catalyzes the 3-hydroxy-3-methylglutaryl coenzyme A to form MVA. In this study, two cDNA sequences of HMGR genes, namely, GbHMGR2 and GbHMGR3, were cloned from G. biloba. The protein sequences of GbHMGR2 and GbHMGR3, which contain several functional domains, were analyzed. Regulatory elements related to light, hormone, and stress response were detected in the promoter regions of GbHMGR2 and GbHMGR3. The catalytic activity of these genes was verified by a functional complement experiment in yeast. Quantitative real-time PCR (qRT-PCR) showed the distinct expression patterns of the two genes in different organs. The TTL contents in the organs were detected by high-performance liquid chromatography- evaporative light scattering detector. GbHMGR2 and GbHMGR3 were responded to cold, dark, methyl jasmonate (MJ), abscisic acid (ABA), salicylic acid (SA), and ethephon (Eth) treatments. The TTL contents were also regulated by cold, dark, MJ, ABA, SA, and Eth treatment. In conclusion, GbHMGR2 and GbHMGR3 may participate in the MVA pathway of TTL biosynthesis.

Involvement of HD-ZIP I transcription factors LcHB2 and LcHB3 in fruitlet abscission by promoting transcription of genes related to the biosynthesis of ethylene and ABA in litchi

Abnormal fruitlet abscission is a limiting factor in the production of litchi, an economically important fruit in Southern Asia. Both ethylene and abscisic acid (ABA) induce organ abscission in plants. Although ACS/ACO and NCED genes are known to encode key enzymes required for ethylene and ABA biosynthesis, respectively, the transcriptional regulation of these genes is unclear in the process of plant organ shedding. Here, two polygalacturonase (PG) genes (LcPG1 and LcPG2) and two novel homeodomain-leucine zipper I transcription factors genes (LcHB2 and LcHB3) were identified as key genes associated with the fruitlet abscission in litchi. The expression of LcPG1 and LcPG2 was strongly associated with litchi fruitlet abscission, consistent with enhanced PG activity and reduced homogalacturonan content in fruitlet abscission zones (FAZs). The promoter activities of LcPG1/2 were enhanced by ethephon and ABA. In addition, the production of ethylene and ABA in fruitlets was significantly increased during fruit abscission. Consistently, expression of five genes (LcACO2, LcACO3, LcACS1, LcACS4 and LcACS7) related to ethylene biosynthesis and one gene (LcNCED3) related to ABA biosynthesis in FAZs were activated. Further, electrophoretic mobility shift assays and transient expression experiments demonstrated that both LcHB2 and LcHB3 could directly bind to the promoter of LcACO2/3, LcACS1/4/7 and LcNCED3 genes and activate their expression. Collectively, we propose that LcHB2/3 are involved in the litchi fruitlet abscission through positive regulation of ethylene and ABA biosynthesis.

Genome-Wide Identification and Expression Analysis of HD-ZIP I Gene Subfamily in Nicotiana tabacum

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.

Field-grown transgenic wheat expressing the sunflower gene HaHB4 significantly outyields the wild type

HaHB4 is a sunflower transcription factor belonging to the homeodomain-leucine zipper I family whose ectopic expression in Arabidopsis triggers drought tolerance. The use of PCR to clone the HaHB4 coding sequence for wheat transformation caused unprogrammed mutations producing subtle differences in its activation ability in yeast. Transgenic wheat plants carrying a mutated version of HaHB4 were tested in 37 field experiments. A selected transgenic line yielded 6% more (P<0.001) and had 9.4% larger water use efficiency (P<0.02) than its control across the evaluated environments. Differences in grain yield between cultivars were explained by the 8% improvement in grain number per square meter (P<0.0001), and were more pronounced in stress (16% benefit) than in non-stress conditions (3% benefit), reaching a maximum of 97% in one of the driest environments. Increased grain number per square meter of transgenic plants was accompanied by positive trends in spikelet numbers per spike, tillers per plant, and fertile florets per plant. The gene transcripts associated with abiotic stress showed that HaHB4's action was not dependent on the response triggered either by RD19 or by DREB1a, traditional candidates related to water deficit responses. HaHB4 enabled wheat to show some of the benefits of a species highly adapted to water scarcity, especially in marginal regions characterized by frequent droughts.