Arabidopsis Cys2/His2-type zinc-finger proteins function as transcription repressors under drought, cold, and high-salinity stress conditions

Identification and expression analysis of CCCH gene family and screening of key low temperature stress response gene CbuC3H24 and CbuC3H58 in Catalpa bungei

Catalpa bungei, a tree indigenous to China, is renowned for its superior timber quality and as an ornamental in horticulture. To promote the cultivation of C. bungei in cold regions and expand its distribution, enhancing its cold tolerance is essential. The CCCH gene family is widely involved in plant growth, development, and expression under stress conditions, including low-temperature stress. However, a comprehensive identification and analysis of these genes have not yet been conducted. This study aims to identify key cold-tolerance-related genes within the CCCH gene family of C. bungei, providing the necessary theoretical support for its expansion in cold regions. In this study, 61 CCCH genes within C. bungei were identified and characterized. Phylogenetic assessment divided these genes into 9 subfamilies, with 55 members mapped across 16 chromosomes. The analysis of gene structures and protein motifs indicated that members within the same subfamily shared similar exon/intron distribution and motif patterns, supporting the phylogenetic classification. Collinearity analysis suggested that segmental duplications have played a significant role in the expansion of the C. bungei CCCH gene family. Notably, RNA sequencing analysis under 4 °C cold stress conditions identified CbuC3H24 and CbuC3H58 as exhibiting the most significant responses, highlighting their importance within the CCCH zinc finger family in response to cold stress. The findings of this study lay a theoretical foundation for further exploring the mechanisms of cold tolerance in C. bungei, providing crucial insights for its cultivation in cold regions.

Characterization of the ZCTs, a subgroup of Cys2-His2 zinc finger transcription factors regulating alkaloid biosynthesis in Catharanthus roseus

KEY MESSAGE

The C. roseus ZCTs are jasmonate-responsive, can be induced by CrMYC2a, and can act as significant regulators of the terpenoid indole alkaloid pathway when highly expressed. Catharanthus roseus is the sole known producer of the anti-cancer terpenoid indole alkaloids (TIAs), vinblastine and vincristine. While the enzymatic steps of the pathway have been elucidated, an understanding of its regulation is still emerging. The present study characterizes an important subgroup of Cys2-His2 zinc finger transcription factors known as Zinc finger Catharanthus Transcription factors (ZCTs). We identified three new ZCT members (named ZCT4, ZCT5, and ZCT6) that clustered with the putative repressors of the TIA pathway, ZCT1, ZCT2, and ZCT3. We characterized the role of these six ZCTs as potential redundant regulators of the TIA pathway, and their tissue-specific and jasmonate-responsive expression. These ZCTs share high sequence conservation in their two Cys2-His2 zinc finger domains but differ in the spacer length and sequence between these zinc fingers. The transient overexpression of ZCTs in seedlings significantly repressed the promoters of the terpenoid (pLAMT) and condensation branch (pSTR1) of the TIA pathway, consistent with that previously reported for ZCT1, ZCT2, and ZCT3. In addition, ZCTs significantly repressed and indirectly activated several promoters of the vindoline pathway (not previously studied). The ZCTs differed in their tissue-specific expression but similarly increased with jasmonate in a dosage-dependent manner (except for ZCT5). We showed significant activation of the pZCT1 and pZCT3 promoters by the de-repressed CrMYC2a, suggesting that the jasmonate-responsive expression of the ZCTs can be mediated by CrMYC2a. In summary, the C. roseus ZCTs are jasmonate-responsive, can be induced by CrMYC2a, and can act as significant regulators of the TIA pathway when highly expressed.

Transcriptomic Identification of Potential C2H2 Zinc Finger Protein Transcription Factors in Pinus massoniana in Response to Biotic and Abiotic Stresses

Biotic and abiotic stresses have already seriously restricted the growth and development of Pinus massoniana, thereby influencing the quality and yield of its wood and turpentine. Recent studies have shown that C2H2 zinc finger protein transcription factors play an important role in biotic and abiotic stress response. However, the members and expression patterns of C2H2 TFs in response to stresses in P. massoniana have not been performed. In this paper, 57 C2H2 zinc finger proteins of P. massoniana were identified and divided into five subgroups according to a phylogenetic analysis. In addition, six Q-type PmC2H2-ZFPs containing the plant-specific motif 'QALGGH' were selected for further study under different stresses. The findings demonstrated that PmC2H2-ZFPs exhibit responsiveness towards various abiotic stresses, including drought, NaCl, ABA, PEG, H2O2, etc., as well as biotic stress caused by the pine wood nematode. In addition, PmC2H2-4 and PmC2H2-20 were nuclear localization proteins, and PmC2H2-20 was a transcriptional activator. PmC2H2-20 was selected as a potential transcriptional regulator in response to various stresses in P. massoniana. These findings laid a foundation for further study on the role of PmC2H2-ZFPs in stress tolerance.

The transcription factor MhZAT10 enhances antioxidant capacity by directly activating the antioxidant genes MhMSD1, MhAPX3a and MhCAT1 in apple rootstock SH6 (Malus honanensis × M. domestica)

Stress tolerance in apple (Malus domestica) can be improved by grafting to a stress-tolerant rootstock, such as 'SH6' (Malus honanensis × M. domestica 'Ralls Genet'). However, the mechanisms of stress tolerance in this rootstock are unclear. In Arabidopsis (Arabidopsis thaliana), the transcription factor ZINC FINGER OF ARABIDOPSIS THALIANA 10 is a key component of plant tolerance to multiple abiotic stresses and positively regulates antioxidant enzymes. However, how reactive oxygen species are eliminated upon activation of ZINC FINGER OF ARABIDOPSIS THALIANA 10 in response to abiotic stress remains elusive. Here, we report that MhZAT10 in the rootstock SH6 directly activates the transcription of three genes encoding the antioxidant enzymes MANGANESE SUPEROXIDE DISMUTASE 1 (MhMSD1), ASCORBATE PEROXIDASE 3A (MhAPX3a) and CATALASE 1 (MhCAT1) by binding to their promoters. Heterologous expression in Arabidopsis protoplasts showed that MhMSD1, MhAPX3a and MhCAT1 localize in multiple subcellular compartments. Overexpressing MhMSD1, MhAPX3a or MhCAT1 in SH6 fruit calli resulted in higher superoxide dismutase, ascorbate peroxidase and catalase enzyme activities in their respective overexpressing calli than in those overexpressing MhZAT10. Notably, the calli overexpressing MhZAT10 exhibited better growth and lower reactive oxygen species levels under simulated osmotic stress. Apple SH6 plants overexpressing MhZAT10 in their roots via Agrobacterium rhizogenes-mediated transformation also showed enhanced tolerance to osmotic stress, with higher leaf photosynthetic capacity, relative water content in roots and antioxidant enzyme activity, as well as less reactive oxygen species accumulation. Overall, our study demonstrates that the transcription factor MhZAT10 synergistically regulates the transcription of multiple antioxidant-related genes and elevates reactive oxygen species detoxification.

Identification and expression of the Di19 gene family in response to abiotic stress in common bean (Phaseolus vulgaris L.)

Drought-induced 19 (Di19) protein plays critical biological functions in response to adversity as well as in plant growth and development. Exploring the role and mechanism of Di19 in abiotic stress responses is of great significance for improving plant tolerance. In this study, six Di19 genes were identified in the common bean (Phaseolus vulgaris L.), which were mainly derived from segmental duplications. These genes share conserved exon/intron structures and were classified into three subfamilies based on their phylogenetic relationships. The composition and arrangement of conserved motifs were consistent with their phylogenetic relationships. Many hormone- and stress-responsive elements were distributed in the promoters region of PvDi19 genes. Variations in histidine residues in the Cys2/His2 (C2H2) zinc-finger domains resulted in an atypical tertiary structure of PvDi19-5. Gene expression analysis showed rapid induction of PvDi19-1 in roots by 10% PEG treatment, and PvDi19-2 in leaves by 20% PEG treatment, respectively. Most PvDi19s exhibited insensitivity to saline-alkali stress, except for PvDi19-6, which was notably induced during later stages of treatment. The most common bean Di19 genes were inhibited or not regulated by cadmium stress, but the expression of PvDi19-6 in roots was significantly upregulated when subjected to lower concentrations of cadmium (5 mmol). Moreover, Di19s exhibited greater sensitivity to severe cold stress (6°C). These findings enhance our understanding of the role of PvDi19s in common bean abiotic stress responses and provide a basis for future genetic enhancements in common bean stress tolerance.

MrERF039 transcription factor plays an active role in the cold response of Medicago ruthenica as a sugar molecular switch

Cold stress severely restricts plant development, causing significant agricultural losses. We found a critical transcription factor network in Medicago ruthenica was involved in plant adaptation to low-temperature. APETALA2/ethylene responsive factor (AP2/ERF) transcription factor MrERF039 was transcriptionally induced by cold stress in M. ruthenica. Overexpression of MrERF039 significantly increased the glucose and maltose content, thereby improving the tolerance of M. ruthenica. MrERF039 could bind to the DRE cis-acting element in the MrCAS15A promoter. Additionally, the methyl group of the 14th amino acid in MrERF039 was required for binding. Transcriptome analysis showed that MrERF039 acted as a sugar molecular switch, regulating numerous sugar transporters and sugar metabolism-related genes. In addition, we found that MrERF039 could directly regulate β-amylase gene, UDP glycosyltransferase gene, and C2H2 zinc finger protein gene expression. In conclusion, these findings suggest that high expression of MrERF039 can significantly improve the cold tolerance of M. ruthenica root tissues during cold acclimation. Our results provide a new theoretical basis and candidate genes for breeding new legume forage varieties with high resistance.

Genome-wide analysis of C2H2 zinc finger family and their response to abiotic stresses in apple

C2H2-type zinc finger proteins are one of the most widely studied families in plants and play important roles in abiotic stress responses. In the present study, the physicochemical properties, chromosomal locations, evolutionary relationships, and gene structures of 54 C2H2 zinc finger protein (ZFP) family members were analyzed in apple. The MdC2H2-ZFP genes were phylogenetically clustered into seven subfamilies distributed in different densities on 16 chromosomes. The RNA-seq data from various tissues revealed that MdC2H2-ZFPs differentially expressed among root, stem, leaf, flower, and fruits. Quantitative analysis of its expression characteristics showed that the MdC2H2-ZFP genes were rapidly induced as exposure to abiotic stresses such as drought, salt and low temperature etc. Under drought stress, the expression of eight members was significantly up-regulated, and the highest was obtained from MdC2H2-17; as exposure to salt stress, nine MdC2H2-ZFPs was obviously up-regulated, with the highest expression of MdC2H2-13; and under low temperature stress, the expression of seven members was highly up-regulated, and MdC2H2-13 also demonstrated the highest expression which is same as the case under salt stress. Therefore, some members of MdC2H2-ZFP gene family considerably involve in the multiple abiotic stress responses, which may better understand the function of this family and facilitate the breeding of apple for stress tolerance.

Regulatory networks in plant responses to drought and cold stress

Drought and cold represent distinct types of abiotic stress, each initiating unique primary signaling pathways in response to dehydration and temperature changes, respectively. However, a convergence at the gene regulatory level is observed where a common set of stress-responsive genes is activated to mitigate the impacts of both stresses. In this review, we explore these intricate regulatory networks, illustrating how plants coordinate distinct stress signals into a collective transcriptional strategy. We delve into the molecular mechanisms of stress perception, stress signaling, and the activation of gene regulatory pathways, with a focus on insights gained from model species. By elucidating both the shared and distinct aspects of plant responses to drought and cold, we provide insight into the adaptive strategies of plants, paving the way for the engineering of stress-resilient crop varieties that can withstand a changing climate.

Genome-wide identification, characterization and expression of C2H2 zinc finger gene family in Opisthopappus species under salt stress

BACKGROUND

The C2H2 zinc finger protein family plays important roles in plants. However, precisely how C2H2s function in Opisthopappus (Opisthopappus taihangensis and Opisthopappus longilobus) remains unclear.

RESULTS

In this study, a total of 69 OpC2H2 zinc finger protein genes were identified and clustered into five Groups. Seven tandem and ten fragment repeats were found in OpC2H2s, which underwent robust purifying selection. Of the identified motifs, motif 1 was present in all OpC2H2s and conserved at important binding sites. Most OpC2H2s possessed few introns and exons that could rapidly activate and react when faced with stress. The OpC2H2 promoter sequences mainly contained diverse regulatory elements, such as ARE, ABRE, and LTR. Under salt stress, two up-regulated OpC2H2s (OpC2H2-1 and OpC2H2-14) genes and one down-regulated OpC2H2 gene (OpC2H2-7) might serve as key transcription factors through the ABA and JA signaling pathways to regulate the growth and development of Opisthopappus species.

CONCLUSION

The above results not only help to understand the function of C2H2 gene family but also drive progress in genetic improvement for the salt tolerance of Opisthopappus species.

Expression of the Arabidopsis redox-related LEA protein, SAG21 is regulated by ERF, NAC and WRKY transcription factors

SAG21/LEA5 is an unusual late embryogenesis abundant protein in Arabidopsis thaliana, that is primarily mitochondrially located and may be important in regulating translation in both chloroplasts and mitochondria. SAG21 expression is regulated by a plethora of abiotic and biotic stresses and plant growth regulators indicating a complex regulatory network. To identify key transcription factors regulating SAG21 expression, yeast-1-hybrid screens were used to identify transcription factors that bind the 1685 bp upstream of the SAG21 translational start site. Thirty-three transcription factors from nine different families bound to the SAG21 promoter, including members of the ERF, WRKY and NAC families. Key binding sites for both NAC and WRKY transcription factors were tested through site directed mutagenesis indicating the presence of cryptic binding sites for both these transcription factor families. Co-expression in protoplasts confirmed the activation of SAG21 by WRKY63/ABO3, and SAG21 upregulation elicited by oligogalacturonide elicitors was partially dependent on WRKY63, indicating its role in SAG21 pathogen responses. SAG21 upregulation by ethylene was abolished in the erf1 mutant, while wound-induced SAG21 expression was abolished in anac71 mutants, indicating SAG21 expression can be regulated by several distinct transcription factors depending on the stress condition.

ZmC2H2-149 negatively regulates drought tolerance by repressing ZmHSD1 in maize

Drought is a major abiotic stress that limits maize production worldwide. Therefore, it is of great importance to improve drought tolerance in crop plants for sustainable agriculture. In this study, we examined the roles of Cys2 /His2 zinc-finger-proteins (C2H2-ZFPs) in maize's drought tolerance as C2H2-ZFPs have been implicated for plant stress tolerance. By subjecting 150 Ac/Ds mutant lines to drought stress, we successfully identified a Ds-insertion mutant, zmc2h2-149, which shows increased tolerance to drought stress. Overexpression of ZmC2H2-149 in maize led to a decrease in both drought tolerance and crop yield. DAP-Seq, RNA-Seq, Y1H and LUC assays additionally showed that ZmC2H2-149 directly suppresses the expression of a positive drought tolerance regulator, ZmHSD1 (hydroxysteroid dehydrogenase 1). Consistently, the zmhsd1 mutants exhibited decreased drought tolerance and grain yield under water deficit conditions compared to their respective wild-type plants. Our findings thus demonstrated that ZmC2H2-149 can regulate ZmHSD1 for drought stress tolerance in maize, offering valuable theoretical and genetic resources for maize breeding programmes that aim for improving drought tolerance.

RNA-Seq-Based WGCNA and Association Analysis Reveal the Key Regulatory Module and Genes Responding to Salt Stress in Wheat Roots

Soil salinization is the main abiotic stressor faced by crops. An improved understanding of the transcriptional response to salt stress in roots, the organ directly exposed to a high salinity environment, can inform breeding strategies to enhance tolerance and increase crop yield. Here, RNA-sequencing was performed on the roots of salt-tolerant wheat breeding line CH7034 at 0, 1, 6, 24, and 48 h after NaCl treatment. Based on transcriptome data, a weighted gene co-expression network analysis (WGCNA) was constructed, and five gene co-expression modules were obtained, of which the blue module was correlated with the time course of salt stress at 1 and 48 h. Two GO terms containing 249 differentially expressed genes (DEGs) related to osmotic stress response and salt-stress response were enriched in the blue module. These DEGs were subsequently used for association analysis with a set of wheat germplasm resources, and the results showed that four genes, namely a Walls Are Thin 1-related gene (TaWAT), an aquaporin gene (TaAQP), a glutathione S-transfer gene (TaGST), and a zinc finger gene (TaZFP), were associated with the root salt-tolerance phenotype. Using the four candidate genes as hub genes, a co-expression network was constructed with another 20 DEGs with edge weights greater than 0.6. The network showed that TaWAT and TaAQP were mainly co-expressed with fifteen interacting DEGs 1 h after salt treatment, while TaGST and TaZFP were mainly co-expressed with five interacting DEGs 48 h after salt treatment. This study provides key modules and candidate genes for understanding the salt-stress response mechanism in wheat roots.

PtoMYB031, the R2R3 MYB transcription factor involved in secondary cell wall biosynthesis in poplar

Introduction

The biosynthesis of the secondary cell wall (SCW) is orchestrated by an intricate hierarchical transcriptional regulatory network. This network is initiated by first-layer master switches, SCW-NAC transcription factors, which in turn activate the second-layer master switches MYBs. These switches play a crucial role in regulating xylem specification and differentiation during SCW formation. However, the roles of most MYBs in woody plants are yet to be fully understood.

Methods

In this study, we identified and isolated the R2R3-MYB transcription factor, PtoMYB031, from Populus tomentosa. We explored its expression, mainly in xylem tissues, and its role as a transcriptional repressor in the nucleus. We used overexpression and RNA interference techniques in poplar, along with Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays, to analyze the regulatory effects of PtoMYB031.

Results

Overexpression of PtoMYB031 in poplar significantly reduced lignin, cellulose, and hemicellulose content, and inhibited vascular development in stems, resulting in decreased SCW thickness in xylem tissues. Gene expression analysis showed that structural genes involved in SCW biosynthesis were downregulated in PtoMYB031-OE lines. Conversely, RNA interference of PtoMYB031 increased these compounds. Additionally, PtoMYB031 was found to recruit the repressor PtoZAT11, forming a transcriptional inhibition complex.

Discussion

Our findings provide new insights into how PtoMYB031, through its interaction with PtoZAT11, forms a complex that can suppress the expression of key regulatory genes, PtoWND1A and PtoWND2B, in SCW biosynthesis. This study enhances our understanding of the transcriptional regulation involved in SCW formation in poplar, highlighting the significant role of PtoMYB031.

Zinc finger transcription factor MtZPT2-2 negatively regulates salt tolerance in Medicago truncatula

Zinc finger proteins (ZFPs) are transcription factors involved in multiple cellular functions. We identified a C2H2 type ZFP (MtZPT2-2) in Medicago truncatula and demonstrated that it localizes to the nucleus and inhibits the transcription of 2 genes encoding high-affinity potassium transporters (MtHKT1;1 and MtHKT1;2). MtZPT2-2 transcripts were detected in stem, leaf, flower, seeds and roots, with the highest level in the xylem and phloem of roots and stems. MtZPT2-2 transcription in leaves was reduced after salt stress. Compared with the wild-type (WT), transgenic lines overexpressing MtZPT2-2 had decreased salt tolerance, while MtZPT2-2-knockout mutants showed increased salt tolerance. MtHKT1;1 and MtHKT1;2 transcripts and Na+ accumulation in shoots and roots, as well as in the xylem of all genotypes of plants, were increased after salt treatment, with higher levels of MtHKT1;1 and MtHKT1;2 transcripts and Na+ accumulation in MtZPT2-2-knockout mutants and lower levels in MtZPT2-2-overexpressing lines compared with the WT. K+ levels showed no significant difference among plant genotypes under salt stress. Moreover, MtZPT2-2 was demonstrated to bind with the promoter of MtHKT1;1 and MtHKT1;2 to inhibit their expression. Antioxidant enzyme activities and the gene transcript levels were accordingly upregulated in response to salt, with higher levels in MtZPT2-2-knockout mutants and lower levels in MtZPT2-2-overexpressing lines compared with WT. The results suggest that MtZPT2-2 regulates salt tolerance negatively through downregulating MtHKT1;1 and MtHKT1;2 expression directly to reduce Na+ unloading from the xylem and regulates antioxidant defense indirectly.

Blue Light Exposure Caused Large-Scale Transcriptional Changes in the Abdomen and Reduced the Reproductive Fitness of the Fall Armyworm Spodoptera frugiperda

In the present study, we found that blue light stress negatively affected the development periods, body weight, survival and reproduction of Spodoptera frugiperda, and it showed a dose-dependent reaction, as longer irradiation caused severer effects. Further transcriptome analysis found blue light stress induced fast and large-scale transcriptional changes in the head, thorax and, particularly, the abdomen of female S. frugiperda adults. A functional enrichment analysis indicated that shorter durations of blue light irradiation induced the upregulation of more stress response- and defense-related genes or pathways, such as abiotic stimuli detection and response, oxidative stress, ion channels and protein-kinase-based signal pathways. In the abdomen, however, different durations of blue-light-exposure treatments all induced the downregulation of a large number genes and pathways related to cellular processes, metabolism, catalysis and reproduction, which may be a trade-off between antistress defense and other processes or a strategy to escape stressful conditions. These results indicate irradiation duration- and tissue-specific blue light stress responses and consequences, as well as suggest that the stress that results in transcriptional alterations is associated with the stress that causes a fitness reduction in S. frugiperda females.

Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensis

BACKGROUND

Drought is one of the main consequences of global climate change and this problem is expected to intensify in the future. Resurrection plants evolved the ability to withstand the negative impact of long periods of almost complete desiccation and to recover at rewatering. In this respect, many physiological, transcriptomic, proteomic and genomic investigations have been performed in recent years, however, few epigenetic control studies have been performed on these valuable desiccation-tolerant plants so far.

RESULTS

In the present study, for the first time for resurrection plants we provide evidences about the differential chromatin accessibility of Haberlea rhodopensis during desiccation stress by ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput sequencing). Based on gene similarity between species, we used the available genome of the closely related resurrection plant Dorcoceras hygrometricum to identify approximately nine hundred transposase hypersensitive sites (THSs) in H. rhodopensis. The majority of them corresponds to proximal and distal regulatory elements of different genes involved in photosynthesis, carbon metabolism, synthesis of secondary metabolites, cell signalling and transcriptional regulation, cell growth, cell wall, stomata conditioning, chaperons, oxidative stress, autophagy and others. Various types of binding motifs recognized by several families of transcription factors have been enriched from the THSs found in different stages of drought. Further, we used the previously published RNA-seq data from H. rhodopensis to evaluate the expression of transcription factors putatively interacting with the enriched motifs, and the potential correlation between the identified THS and the expression of their corresponding genes.

CONCLUSIONS

These results provide a blueprint for investigating the epigenetic regulation of desiccation tolerance in resurrection plant H. rhodopensis and comparative genomics between resurrection and non-resurrection species with available genome information.

High and Low Temperatures Differentially Affect Survival, Reproduction, and Gene Transcription in Male and Female Moths of Spodoptera frugiperda

In this study, we found that both heat and cold stresses significantly affected the survival and reproduction of both sexes in Spodoptera frugiperda adults, with larvae showing relatively higher extreme temperature tolerance. Further transcriptomic analysis in adults found remarkable differences and similarities between sexes in terms of temperature stress responses. Metabolism-related processes were suppressed in heat stressed females, which did not occur to the same extend in males. Moreover, both heat and cold stress reduced immune activities in both sexes. Heat stress induced the upregulation of many heat shock proteins in both sexes, whereas the response to cold stress was insignificant. More cold tolerance-related genes, such as cuticle proteins, UDP-glucuronosyltransferase, and facilitated trehalose transporter Tret1, were found upregulated in males, whereas most of these genes were downregulated in females. Moreover, a large number of fatty acid-related genes, such as fatty acid synthases and desaturases, were differentially expressed under heat and cold stresses in both sexes. Heat stress in females induced the upregulation of a large number of zinc finger proteins and reproduction-related genes; whereas cold stress induced downregulation in genes linked to reproduction. In addition, TRPA1-like encoding genes (which have functions involved in detecting temperature changes) and sex peptide receptor-like genes were found to be differentially expressed in stressed moths. These results indicate sex-specific heat and cold stress responses and adaptive mechanisms and suggest sex-specific trade-offs between stress-resistant progresses and fundamental metabolic processes as well as between survival and reproduction.

Melatonin alleviates aluminum toxicity by regulating aluminum-responsive and nonresponsive pathways in hickory

Aluminum (Al) toxicity is a significant constraint on agricultural productivity worldwide. Melatonin (MT) has been shown to alleviate Al toxicity in plants; however, the underlying mechanisms remain largely unknown. Here, we employed a combination of physiological and molecular biology techniques to examine the role of MT in mitigating Al toxicity of hickory. We found that MT decreased the contents of cell wall pectin, hemicellulose, Al, and Al-induced massive reactive oxygen species accumulation in the roots of hickory. Transcriptomic analysis revealed that MT may alleviate root tip Al stress by regulating Al-responsive and nonresponsive pathways. Co-expression regulatory network and dual-luciferase receptor assays revealed that transcription factors, CcC3H12 and CcAZF2, responded to MT and significantly activated the expression of two cell wall pectin-related genes, CcPME61 and CcGAE6, respectively. Further, yeast one-hybrid and electrophoretic mobility shift assay (EMSA) assays verified that CcC3H12 and CcAZF2 regulated CcPME61 and CcGAE6, respectively, by directly binding to their promoters. Overexpression of CcPME61 enhanced the Al sensitivity of Arabidopsis thaliana. Our results indicate that MT can improve Al tolerance of hickory via multiple pathways, which provides a new perspective for the study of the mechanism of MT in alleviating abiotic stress.

QTLs and Candidate Loci Associated with Drought Tolerance Traits of Kaybonnet x ZHE733 Recombinant Inbred Lines Rice Population

Rice is the most important staple crop for the sustenance of the world's population, and drought is a major factor limiting rice production. Quantitative trait locus (QTL) analysis of drought-resistance-related traits was conducted on a recombinant inbred line (RIL) population derived from the self-fed progeny of a cross between the drought-resistant tropical japonica U.S. adapted cultivar Kaybonnet and the drought-sensitive indica cultivar ZHE733. K/Z RIL population of 198 lines was screened in the field at Fayetteville (AR) for three consecutive years under controlled drought stress (DS) and well-watered (WW) treatment during the reproductive stage. The effects of DS were quantified by measuring morphological traits, grain yield components, and root architectural traits. A QTL analysis using a set of 4133 single nucleotide polymorphism (SNP) markers and the QTL IciMapping identified 41 QTLs and 184 candidate genes for drought-related traits within the DR-QTL regions. RT-qPCR in parental lines was used to confirm the putative candidate genes. The comparison between the drought-resistant parent (Kaybonnet) and the drought-sensitive parent (ZHE733) under DS conditions revealed that the gene expression of 15 candidate DR genes with known annotations and two candidate DR genes with unknown annotations within the DR-QTL regions was up-regulated in the drought-resistant parent (Kaybonnet). The outcomes of this research provide essential information that can be utilized in developing drought-resistant rice cultivars that have higher productivity when DS conditions are prevalent.

Genome-Wide Identification and Analysis of the Genes Encoding Q-Type C2H2 Zinc Finger Proteins in Grapevine

Q-type C2H2 zinc finger proteins (ZFPs), the largest family of transcription factors, have been extensively studied in plant genomes. However, the genes encoding this transcription factor family have not been explored in grapevine genomes. Therefore, in this study, we conducted a genome-wide identification of ZFP genes in three species of grapevine, namely Vitis vinifera, Vitis riparia, and Vitis amurensis, based on the sequence databases and phylogenetic and their conserved domains. We identified 52, 54, and 55 members of Q-type C2H2 ZFPs in V. vinifera, V. riparia, and V. amurensis, respectively. The physical and chemical properties of VvZFPs, VrZFPs, and VaZFPs were examined. The results showed that these proteins exhibited differences in the physical and chemical properties and that they all were hydrophobic proteins; the instability index showed that the four proteins were stable. The subcellular location of the ZFPs in the grapevine was predicted mainly in the nucleus. The phylogenetic tree analysis of the amino acid sequences of VvZFP, VaZFP, VrZFP, and AtZFP proteins showed that they were closely related and were divided into six subgroups. Chromosome mapping analysis showed that VvZFPs, VrZFPs, and VaZFPs were unevenly distributed on different chromosomes. The clustered gene analysis showed that the motif distribution was similar and the sequence of genes was highly conserved. Exon and intron structure analysis showed that 118 genes of ZFPs were intron deletion types, and the remaining genes had variable numbers of introns, ranging from 2 to 15. Cis-element analysis showed that the promoter of VvZFPs contained multiple cis-elements related to plant hormone response, stress resistance, and growth, among which the stress resistance elements were the predominant elements. Finally, the expression of VvZFP genes was determined using real-time quantitative PCR, which confirmed that the identified genes were involved in response to methyl jasmonate (MeJA), abscisic acid (ABA), salicylic acid (SA), and low-temperature (4 °C) stress. VvZFP10-GFP and VvZFP46-GFP fusion proteins were localized in the nucleus of tobacco cells, and VvZFP10 is the most responsive gene among all VvZFPs with the highest relative expression level to MeJA, ABA, SA and low-temperature (4 °C) stress. The present study provides a theoretical basis for exploring the mechanism of response to exogenous hormones and low-temperature tolerance in grapes and its molecular breeding in the future.

Genome-Wide Analysis of Q-Type C2H2 ZFP Genes in Response to Biotic and Abiotic Stresses in Sugar Beet

A plant's Q-type C2H2-type ZFP plays key roles in plant growth and development and responses to biotic and abiotic stresses. Sugar beet (Beta vulgaris L.) is an important crop for sugar production. Salt stress and viral infection significantly reduce the root yield and sugar content of sugar beet. However, there is a lack of comprehensive genome-wide analyses of Q-type C2H2 ZFPs and their expression patterns in sugar beet under stress. In this study, 35 sugar beet Q-type C2H2 ZFPs (BvZFPs) containing at least one conserved "QALGGH" motif were identified via bioinformatics techniques using TBtools software. According to their evolutionary relationship, the BvZFPs were classified into five subclasses. Within each subclass, the physicochemical properties and motif compositions showed strong similarities. A Ka/Ks analysis indicated that the BvZFPs were conserved during evolution. Promoter cis-element analysis revealed that most BvZFPs are associated with elements related to phytohormone, biotic or abiotic stress, and plant development. The expression data showed that the BvZFPs in sugar beet are predominantly expressed in the root. In addition, BvZFPs are involved in the response to abiotic and biotic stresses, including salt stress and viral infection. Overall, these results will extend our understanding of the Q-type C2H2 gene family and provide valuable information for the biological breeding of sugar beet against abiotic and biotic stresses in the future.

Whole-genome identification and multiple abiotic stresses expression pattern profiling analysis of PLATZ transcription factor family members in Pecan (Carya illinoensis)

Plant AT-rich sequence and zinc-binding (PLATZ), as a plant-specific transcription factor, have been identified and studied in a variety of plants. However, there are no reports about PLATZ proteins in Carya illinoensis (pecan). Here, 24 C. illinoensis CiPLATZs have been identified and divided into 4 groups. Gene structure, motif composition, conserved domain and cis-acting elements analysis indicated that the PLATZ gene family was highly conserved. Transcriptome data combined with qRT-PCR analysis revealed that CiPLATZ6, CiPLATZ12, CiPLATZ13, CiPLATZ14 and CiPLATZ23 were highly expressed in multiple tissues of C. illinoensis and strongly responded to drought, salt and heat stress. Among them, CiPLATZ6, CiPLATZ12 and CiPLATZ23 were all located in the nucleus and had no transcriptional autoactivation ability in yeast cells, and acted as transcriptional suppressors in plants. In addition, the CiPLATZ23-overexpressing transgenic Arabidopsis thaliana showed enhanced tolerance to drought. Measurements of physiological indicators and analysis of stress-related genes expression levels in transgenic A. thaliana were used to support this conclusion. The results of this study are helpful to understand the structural feature and function of CiPLATZs, and provide candidate genes for molecular breeding of drought tolerance of C. illinoensis.

Heterologous expression of the Glycine soja Kunitz-type protease inhibitor GsKTI improves resistance to drought stress and Helicoverpa armigera in transgenic Arabidopsis lines

Kunitz-like protease inhibitors (KTIs) have been identified to play critical roles in insect defense, but evidence for their involvement in drought stress is sparse. The aim of this study was to identify and functionally characterize a Kunitz-like protease inhibitor, GsKTI, from the wild soybean (Glycine soja) variety ED059. Expression patterns suggest that drought stress and insect herbivory may induce GsKTI transcript levels. Transgenic Arabidopsis lines overexpressing GsKTI have been shown to exhibit enhanced drought tolerance by regulating the ABA signaling pathway and increasing xylem cell number. Transgenic Arabidopsis leaves overexpressing GsKTI interfered with insect digestion and thus had a negative effect on the growth of Helicoverpa armigera. It is concluded that GsKTI increases resistance to drought stress and insect attack in transgenic Arabidopsis lines.

Serotonin: A frontline player in plant growth and stress responses

Serotonin is a well-studied pineal hormone that functions as a neurotransmitter in mammals and is found in varying amounts in diverse plant species. By modulating gene and phytohormonal crosstalk, serotonin has a significant role in plant growth and stress response, including root, shoot, flowering, morphogenesis, and adaptability responses to numerous environmental signals. Despite its prevalence and importance in plant growth and development, its molecular action, regulation and signalling processes remain unknown. Here, we highlight the current knowledge of the role of serotonin-mediated regulation of plant growth and stress response. We focus on serotonin and its regulatory connections with phytohormonal crosstalk and address their possible functions in coordinating diverse phytohormonal responses during distinct developmental phases, correlating with melatonin. Additionally, we have also discussed the possible role of microRNAs (miRNAs) in the regulation of serotonin biosynthesis. In summary, serotonin may act as a node molecule to coordinate the balance between plant growth and stress response, which may shed light on finding its key regulatory pathways for uncovering its mysterious molecular network.

Genome-Wide Analysis of ZAT Gene Family in Osmanthus fragrans and the Function Exploration of OfZAT35 in Cold Stress

Osmanthus fragrans is a popular ornamental and odorant plant with high commercial value, but its cultivation and exploitation are limited by low temperature. The ZAT (zinc finger of Arabidopsis thaliana) genes as a subclass of the C2H2-type zinc finger proteins (C2H2-ZFP) family play essential roles in various abiotic stresses. However, their roles in cold stress response in O. fragrans remain unclear. This study identified 38 OfZATs, which could be divided into 5 subgroups based on the phylogenetic tree, with OfZATs in the same subgroup harboring similar gene structures and motif patterns. In addition, 49 segmental and 5 tandem duplication events were detected among OfZAT genes, while some OfZAT genes exhibited specific expression patterns in different tissues. Furthermore, two OfZATs were induced in salt stress and eight OfZATs responded to cold stress. Interestingly, OfZAT35 showed a continuously increasing expression trend under cold stress, while its protein showed nucleus localization with no transcriptional activation activity. Transiently transformed tobacco overexpressing OfZAT35 exhibited a significantly higher relative electrolyte leakage (REL) level and increased activities of superoxide dismutase (SOD), peroxidase (POD), and Ascorbate peroxidase (APX), while there was significantly decreased activity of catalase (CAT). Moreover, CAT, DREB3, and LEA5, which are associated with cold stress, were dramatically decreased after cold treatment in transiently transformed tobacco, suggesting that overexpression of OfZAT35 negatively regulated cold stress. This study provides a basis for exploring the roles of ZAT genes and contributes to uncovering the mechanism of ZAT-mediated cold stress response in O. fragrans.

Identification of C2H2 zinc finger genes through genome-wide association study and functional analyses of LkZFPs in response to stresses in Larix kaempferi

BACKGROUND

C2H2 zinc finger proteins (C2H2-ZFPs), one of the largest transcription factors, play a variety of roles in plant development and growth as well as stress response. While, the evolutionary history and expression profile of the C2H2-ZFP genes in Larix kaempferi (LkZFPs) have not been reported so far.

RESULTS

In this study, the whole genome of the LkZFPs was identified and characterized, including physicochemical properties, phylogenetic relationships, conservative motifs, the promoter cis-elements and Gene Ontology (GO) annotation. We identified 47 LkZFPs and divided them into four subfamilies based on phylogenetic analysis and conserved motifs. Subcellular localization prediction showed that most of the LkZFPs were located in the nucleus. Promoter cis-element analysis suggested that the LkZFPs may be involved in the regulation of stress responses. Moreover, Real-time quantitative PCR (RT-qPCR) results showed that Q-type LkZFP genes were involved in the response to abiotic stress, such as salt, drought and hormone stresses. Subcellular localization results showed that LkZFP7 and LkZFP37 were located in the nucleus, LkZFP32 was located in both cytoplasm and nucleus.

CONCLUSION

The identification and functional analysis of LkZFPs suggested that some LkZFP genes might play important roles in coping with both biological and abiotic stresses. These results could further increase understanding of the function of the LkZFPs, and provide some research direction and theoretical support.

Transcription factors MhDREB2A/MhZAT10 Play a Role in Drought and Cold Stress Response Crosstalk in Apple

Drought and cold stresses seriously affect tree growth and fruit yield during apple (Malus domestica) production, with combined stress causing injury such as shoot shriveling. However, the molecular mechanism underlying crosstalk between responses to drought and cold stress remains to be clarified. In this study, we characterized the zinc finger transcription factor ZINC FINGER OF ARABIDOPSIS THALIANA 10 (ZAT10) through comparative analysis of shoot-shriveling tolerance between tolerant and sensitive apple rootstocks. MhZAT10 responded to both drought and cold stress. Heterologous expression of MhZAT10 in the sensitive rootstock 'G935' from domesticated apple (Malus domestica) promoted shoot-shriveling tolerance, while silencing of MhZAT10 expression in the tolerant rootstock 'SH6' of Malus honanensis reduced stress tolerance. We determined that the apple transcription factor DEHYDRATION RESPONSE ELEMENT-BINDING PROTEIN 2A (DREB2A) is a direct regulator activating the expression of MhZAT10 in response to drought stress. Apple plants overexpressing both MhDREB2A and MhZAT10 genes exhibited enhanced tolerance to drought and cold stress, while plants overexpressing MhDREB2A but with silenced expression of MhZAT10 showed reduced tolerance, suggesting a critical role of MhDREB2A-MhZAT10 in the crosstalk between drought and cold stress responses. We further identified drought-tolerant MhWRKY31 and cold-tolerant MhMYB88 and MhMYB124 as downstream regulatory target genes of MhZAT10. Our findings reveal a MhDREB2A-MhZAT10 module involved in crosstalk between drought and cold stress responses, which may have applications in apple rootstock breeding programs aimed at developing shoot-shriveling tolerance.

Overexpression of the cotton trihelix transcription factor GhGT23 in Arabidopsis mediates salt and drought stress tolerance by binding to GT and MYB promoter elements in stress-related genes

Cotton (Gossypium hirsutum L.) is the world's most economically valuable textile crop. However, cotton plants are often subjected to numerous abiotic stresses that can dramatically limit yield. Trihelix transcription factors (TTFs) play important roles in abiotic stress responses in many plant species, and efforts to better understand their roles in cotton abiotic stress responses are ongoing. In this study, a member of the cotton TTF family (GhGT23) was functionally characterized. This protein contains a SANT domain and is a member of the SIP subfamily of TTF proteins. GhGT23 was significantly (p < 0.05) and highly expressed in cotton fiber compared to relatively low expression in other tissues. A significant (p < 0.05) increase in GhGT23 expression occurred in cotton seedlings within 12 hours of drought, salt, and ABA exposure. The GhGT23 protein localized in the nucleus but exhibited no signs of transactivation activity. GhGT23 overexpression in Arabidopsis conferred enhanced drought and salt stress tolerance. The expression of stress-related genes was higher in transgenic Arabidopsis expressing GhGT23 than in wild-type plants subjected to salt stress. The results of electrophoretic mobility shift assay revealed that GhGT23 could bind to the GT cis-elements GT-1Box (Box II), GT2-Box, GT3-Box, GT-3a (Site1-type), GT-3b, and Box as well as the MYB cis-elements MBS1 and MRE4. Our results demonstrate that GhGT23 positively regulates salt and drought stress responses, possibly by enhancing the expression of stress-related genes.

The intertwining of Zn-finger motifs and abiotic stress tolerance in plants: Current status and future prospects

Environmental stresses such as drought, high salinity, and low temperature can adversely modulate the field crop's ability by altering the morphological, physiological, and biochemical processes of the plants. It is estimated that about 50% + of the productivity of several crops is limited due to various types of abiotic stresses either presence alone or in combination (s). However, there are two ways plants can survive against these abiotic stresses; a) through management practices and b) through adaptive mechanisms to tolerate plants. These adaptive mechanisms of tolerant plants are mostly linked to their signalling transduction pathway, triggering the action of plant transcription factors and controlling the expression of various stress-regulated genes. In recent times, several studies found that Zn-finger motifs have a significant function during abiotic stress response in plants. In the first report, a wide range of Zn-binding motifs has been recognized and termed Zn-fingers. Since the zinc finger motifs regulate the function of stress-responsive genes. The Zn-finger was first reported as a repeated Zn-binding motif, comprising conserved cysteine (Cys) and histidine (His) ligands, in Xenopus laevis oocytes as a transcription factor (TF) IIIA (or TFIIIA). In the proteins where Zn²⁺ is mainly attached to amino acid residues and thus espousing a tetrahedral coordination geometry. The physical nature of Zn-proteins, defining the attraction of Zn-proteins for Zn²⁺, is crucial for having an in-depth knowledge of how a Zn²⁺ facilitates their characteristic function and how proteins control its mobility (intra and intercellular) as well as cellular availability. The current review summarized the concept, importance and mechanisms of Zn-finger motifs during abiotic stress response in plants.

The involvement of AtMKK1 and AtMKK3 in plant-deleterious microbial volatile compounds-induced defense responses

Plant-deleterious microbial volatiles activate the transactivation of hypoxia, MAMPs and wound responsive genes in Arabidopsis thaliana. AtMKK1 and AtMKK3 are involved in the plant-deleterious microbial volatiles-induced defense responses. Microbial volatile compounds (mVCs) are a collection of volatile metabolites from microorganisms with biological effects on all living organisms. mVCs function as gaseous modulators of plant growth and plant health. In this study, the defense events induced by plant-deleterious mVCs were investigated. Enterobacter aerogenes VCs lead to growth inhibition and immune responses in Arabidopsis thaliana. E. aerogenes VCs negatively regulate auxin response and transport gene expression in the root tip, as evidenced by decreased expression of DR5::GFP, PIN3::PIN3-GFP and PIN4::PIN4-GFP. Data from transcriptional analysis suggests that E. aerogenes VCs trigger hypoxia response, innate immune responses and metabolic processes. In addition, the transcript levels of the genes involved in the synthetic pathways of antimicrobial metabolites camalexin and coumarin are increased after the E. aerogenes VCs exposure. Moreover, we demonstrate that MKK1 serves as a regulator of camalexin biosynthesis gene expression in response to E. aerogenes VCs, while MKK3 is the regulator of coumarin biosynthesis gene expression. Additionally, MKK1 and MKK3 mediate the E. aerogenes VCs-induced callose deposition. Collectively, these studies provide molecular insights into immune responses by plant-deleterious mVCs.

Arabidopsis Cys2/His2 Zinc Finger Transcription Factor ZAT18 Modulates the Plant Growth-Defense Tradeoff

Plant defense responses under unfavorable conditions are often associated with reduced growth. However, the mechanisms underlying the growth-defense tradeoff remain to be fully elucidated, especially at the transcriptional level. Here, we revealed a Cys2/His2-type zinc finger transcription factor, namely, ZAT18, which played dual roles in plant immunity and growth by oppositely regulating the signaling of defense- and growth-related hormones. ZAT18 was first identified as a salicylic acid (SA)-inducible gene and was required for plant responses to SA in this study. In addition, we observed that ZAT18 enhanced the plant immunity with growth penalties that may have been achieved by activating SA signaling and repressing auxin signaling. Further transcriptome analysis of the zat18 mutant showed that the biological pathways of defense-related hormones, including SA, ethylene and abscisic acid, were repressed and that the biological pathways of auxin and cytokinin, which are growth-related hormones, were activated by abolishing the function of ZAT18. The ZAT18-mediated regulation of hormone signaling was further confirmed using qRT-PCR. Our results explored a mechanism by which plants handle defense and growth at the transcriptional level under stress conditions.

MdZAT5 regulates drought tolerance via mediating accumulation of drought-responsive miRNAs and mRNAs in apple

Drought limits apple yield and fruit quality. However, the molecular mechanism of apple in response to drought is not well known. Here, we report a Cys2/His2 (C2H2)-type zinc-finger protein, MdZAT5, that positively regulates apple drought tolerance by regulating drought-responsive RNAs and microRNAs (miRNAs). DNA affinity purification and sequencing and yeast-one hybrid analysis identified the binding motifs of MdZAT5, T/ACACT/AC/A/G. Chromatin immunoprecipitation quantitative polymerase chain reaction (ChIP-qPCR) and electrophoretic mobility shift assays (EMSAs) showed that MdZAT5 directly binds to the promoters of the drought-responsive genes including MdRHA2a, MdLEA14, MdTPX1, and MdCAT3, and activates their expression under drought stress. MdZAT5 interacts with and directly targets HYPONASTIC LEAVES1 (MdHYL1). MdZAT5 may facilitate the interaction of MdHYL1 with pri-miRNAs or MdDCL1 by activating MdHYL1 expression, thereby regulating the biogenesis of drought-responsive miRNAs. Genetic dissection showed that MdHYL1 is essential for MdZAT5-mediated drought tolerance and miRNA biogenesis. In addition, ChIP-qPCR and EMSA revealed that MdZAT5 binds directly to the promoters of some MIR genes including Mdm-miR171i and Mdm-miR172c, and modulates their transcription. Taken together, our findings improve our understanding of the molecular mechanisms of drought response in apple and provide a candidate gene for the breeding of drought-tolerant cultivars.

Genome-Wide Identification of Strawberry C2H2-ZFP C1-2i Subclass and the Potential Function of FaZAT10 in Abiotic Stress

C2H2-type zinc finger proteins (C2H2-ZFPs) play a key role in various plant biological processes and responses to environmental stresses. In Arabidopsisthaliana, C2H2-ZFP members with two zinc finger domains have been well-characterized in response to abiotic stresses. To date, the functions of these genes in strawberries are still uncharacterized. Here, 126 C2H2-ZFPs in cultivated strawberry were firstly identified using the recently sequenced Fragaria × ananassa genome. Among these C2H2-ZFPs, 46 members containing two zinc finger domains in cultivated strawberry were further identified as the C1-2i subclass. These genes were unevenly distributed on 21 chromosomes and classified into five groups according to the phylogenetic relationship, with similar physicochemical properties and motif compositions in the same group. Analyses of conserved domains and gene structures indicated the evolutionary conservation of the C1-2i subclass. A Ka/Ks analysis indicated that the C1-2i members were subjected to purifying selection during evolution. Furthermore, FaZAT10, a typical C2H2-ZFP, was isolated. FaZAT10 was expressed the highest in roots, and it was induced by drought, salt, low-temperature, ABA, and MeJA treatments. It was localized in the nucleus and showed no transactivation activity in yeast cells. Overall, these results provide useful information for enriching the analysis of the ZFPs gene family in strawberry, and they provide support for revealing the mechanism of FaZAT10 in the regulatory network of abiotic stress.

The C2H2-type zinc finger protein PhZFP1 regulates cold stress tolerance by modulating galactinol synthesis in Petunia hybrida

The C2H2 zinc finger proteins (ZFPs) play essential roles in regulating cold stress responses. Similarly, raffinose accumulation contributes to freezing stress tolerance. However, the relationship between C2H2 functions and raffinose synthesis in cold tolerance remains uncertain. Here, we report the characterization of the cold-induced C2H2-type zinc finger protein PhZFP1 in Petunia hybrida. PhZFP1 was found to be predominantly localized in the nucleus. Overexpression of PhZFP1 conferred enhanced cold tolerance in transgenic petunia lines. In contrast, RNAi mediated suppression of PhZFP1 led to increased cold susceptibility. PhZFP1 regulated the expression of a range of abiotic stress responsive-genes including genes encoding proteins involved in reactive oxygen species (ROS) scavenging and raffinose metabolism. The accumulation of galactinol and raffinose, and the levels of PhGolS1-1 transcripts, were significantly increased in PhZFP1-overexpressing plants and decreased in PhZFP1-RNAi plants under cold stress. Moreover, the galactinol synthase (GolS)-encoding gene PhGolS1-1 was identified as a direct target of PhZFP1. Taken together, these results demonstrate that PhZFP1 functions in cold stress tolerance by modulation of galactinol synthesis via regulation of PhGolS1-1. This study also provides new insights into the mechanisms underlying C2H2 zinc finger protein-mediated cold stress tolerance, and has identified a candidate gene for improving cold stress tolerance.

PpZAT5 suppresses the expression of a B-box gene PpBBX18 to inhibit anthocyanin biosynthesis in the fruit peel of red pear

BBX (B-box) proteins play a vital role in light-induced anthocyanin biosynthesis. PpBBX18 was an indispensable regulator for the induction of anthocyanin biosynthesis in the peel of red pear fruit (Pyrus pyrifolia Nakai.). However, the upstream regulation of BBX genes has not been well characterized. In this study, PpZAT5, a cysteine2/histidine2-type transcription factor, was discovered as the upstream negative regulator of PpBBX18. The results showed that PpZAT5 functions as a transcriptional repressor and directly binds to the CAAT motif of PpBBX18 and inhibits its expression. PpZAT5 expression was inhibited by light, which is converse to the expression pattern of anthocyanin-related structural genes. In addition, less anthocyanin accumulated in the PpZAT5-overexpressing pear calli than in the wild-type pear calli; on the contrary, more anthocyanin accumulated in PpZAT5-RNAi pear calli. Moreover, the crucial genes involved in light-induced anthocyanin biosynthesis were markedly down-regulated in the transcriptome of PpZAT5 overexpression pear calli compared to wild-type. In conclusion, our study indicates that PpBBX18 is negatively regulated by a C2H2-type transcriptional repressor, PpZAT5, which reduces anthocyanin content in pear. The present results demonstrate an upstream molecular mechanism of PpBBX18 and provide insights into light-induced anthocyanin biosynthesis.

Genome-wide characterization of C2H2 zinc-finger gene family provides insight into the mechanisms and evolution of the dehydration-rehydration responses in Physcomitrium and Arabidopsis

Dehydration tolerance is a vital factor for land plant evolution and world agricultural production. Numerous studies enlightened that the plant-specific C2H2-type zinc-finger proteins (C2H2-ZFPs) as master regulators played pivotal roles in the abiotic stress responses of plants. However, a comprehensive understanding of the evolution of C2H2-ZFPs in terrestrial plants and its regulatory mechanism in dehydration and rehydration response remains a mystery. In this study, the genome-wide identification of C2H2-ZFP genes revealed 549 homologs in the representatives of terrestrial plant lineages from liverwort to angiosperms. Based on the characteristics of the conserved C2H2-ZF domains, four major C2H2-ZF types (M-, Z-, Q-, and D-type) were identified in the C2H2-ZFPs, with the dominants of M-type in all selected species and followed by Z-type in non-seed plants and Q-type in seed plants, respectively. Phylogenetic analyses of the identified C2H2-ZFPs supported four major groups in the land plant representatives, among which the members from the desiccation-tolerant Physcomitrium patens and the dehydration-sensitive Arabidopsis thaliana displayed different topological relationships in the phylogenies reconstructed for a single species. C2H2-ZFPs clustered in the same subclades shared similar features in their conserved domains and gene structures. Approximately, 81% of the C2H2-ZFP promoters of all 549 identified C2H2-ZFPs harbored the conserved ABA-responsive elements (ABREs) and/or dehydration-responsive elements (DREs). Comparative transcriptomic analyses showed that 50 PpZFPs and 56 AtZFPs significantly changed their transcripts abundance. Interestingly, most of the dehydration- and rehydration-responsive PpZPFs and AtZFPs had been predicted to contain the ABRE and DRE elements in their promoter regions and with over half of which phylogenetically belonging to group III. The differences in the expression patterns of C2H2-ZFPs in responses to dehydration and rehydration between P. patens and A. thaliana reflected their different strategies to adapt to dehydration. The identified candidate PpZFPs were specifically induced by moderate dehydration and reached the peak transcript abundance in severe dehydration. Our study lays the foundations for further functional investigation of C2H2-ZFPs in dehydration responses from an evolutionary perspective in land plants. The findings will provide us with genetic resources and potential targets for drought tolerance breeding in crops and beyond.

Ethanol treatment enhances drought stress avoidance in cassava (Manihot esculenta Crantz)

External application of ethanol enhances tolerance to high salinity, drought, and heat stress in various plant species. However, the effects of ethanol application on increased drought tolerance in woody plants, such as the tropical crop "cassava," remain unknown. In the present study, we analyzed the morphological, physiological, and molecular responses of cassava plants subjected to ethanol pretreatment and subsequent drought stress treatment. Ethanol pretreatment induced a slight accumulation of abscisic acid (ABA) and stomatal closure, resulting in a reduced transpiration rate, higher water content in the leaves during drought stress treatment and the starch accumulation in leaves. Transcriptomic analysis revealed that ethanol pretreatment upregulated the expression of ABA signaling-related genes, such as PP2Cs and AITRs, and stress response and protein-folding-related genes, such as heat shock proteins (HSPs). In addition, the upregulation of drought-inducible genes during drought treatment was delayed in ethanol-pretreated plants compared with that in water-pretreated control plants. These results suggest that ethanol pretreatment induces stomatal closure through activation of the ABA signaling pathway, protein folding-related response by activating the HSP/chaperone network and the changes in sugar and starch metabolism, resulting in increased drought avoidance in plants.

Molecular Pathways of WRKY Genes in Regulating Plant Salinity Tolerance

Salinity is a natural and anthropogenic process that plants overcome using various responses. Salinity imposes a two-phase effect, simplified into the initial osmotic challenges and subsequent salinity-specific ion toxicities from continual exposure to sodium and chloride ions. Plant responses to salinity encompass a complex gene network involving osmotic balance, ion transport, antioxidant response, and hormone signaling pathways typically mediated by transcription factors. One particular transcription factor mega family, WRKY, is a principal regulator of salinity responses. Here, we categorize a collection of known salinity-responding WRKYs and summarize their molecular pathways. WRKYs collectively play a part in regulating osmotic balance, ion transport response, antioxidant response, and hormone signaling pathways in plants. Particular attention is given to the hormone signaling pathway to illuminate the relationship between WRKYs and abscisic acid signaling. Observed trends among WRKYs are highlighted, including group II WRKYs as major regulators of the salinity response. We recommend renaming existing WRKYs and adopting a naming system to a standardized format based on protein structure.

Transcriptional regulatory network of plant cold-stress responses

Recent studies have revealed the complex and flexible transcriptional regulatory network involved in cold-stress responses. Focusing on two major signaling pathways that respond to cold stress, we outline current knowledge of the transcriptional regulatory network and the post-translational regulation of transcription factors in the network. Cold-stress signaling pathways are closely associated with other signaling pathways such as those related to the circadian clock, and large amounts of data on their crosstalk and tradeoffs are available. However, it remains unknown how plants sense and transmit cold-stress signals to regulate gene expression. We discuss recent reports on cold-stress sensing and associated signaling pathways that regulate the network. We also emphasize future directions for developing abiotic stress-tolerant crop plants.

A C2H2-type zinc finger transcription factor, MdZAT17, acts as a positive regulator in response to salt stress

Salt stress restricts plant growth and productivity worldwide. Zinc finger proteins play important roles in response to various abiotic plant stresses. In this research, we identified and characterized the ZAT17 gene in Malus domestica, which encodes a C2H2-type zinc finger protein. MdZAT17 has two typical conserved zinc finger domains and an ERF-associated amphiphilic repression (EAR) motif. Promoter analysis showed that MdZAT17 contains several stress-related response elements (ABRE, CGTCA-motif, and TC-rich repeats), and qRT-PCR analysis showed that the expression level of MdZAT17 was induced by various abiotic stress treatments. The overexpression of MdZAT17 improved tolerance to salt stress in apple calli. The ectopic expression of MdZAT17 in Arabidopsis enhanced salt stress tolerance and led to lower malondialdehyde (MDA) content, lower reactive oxygen species (ROS) accumulation, and greater anthocyanin accumulation under salt stress. Moreover, the overexpression of MdZAT17 transgenic apple calli and Arabidopsis reduced the sensitivity to abscisic acid (ABA). In conclusion, our results indicate that MdZAT17 plays a positive regulatory role in salt tolerance, providing a theoretical basis for further research on its molecular mechanisms.

NbNAC42 and NbZFP3 Transcription Factors Regulate the Virus Inducible NbAGO5 Promoter in Nicotiana benthamiana

Plant argonautes (AGOs) play important roles in the defense responses against viruses. The expression of Nicotiana benthamiana AGO5 gene (NbAGO5) is highly induced by Bamboo mosaic virus (BaMV) infection; however, the underlying mechanisms remain elusive. In this study, we have analyzed the potential promoter activities of NbAGO5 and its interactions with viral proteins by using a 2,000 bp fragment, designated as PN1, upstream to the translation initiation of NbAGO5. PN1 and seven serial 5'-deletion mutants (PN2-PN8) were fused with a β-glucuronidase (GUS) reporter and introduced into the N. benthamiana genome by Agrobacterium-mediated transformation for further characterization. It was found that PN4-GUS transgenic plants were able to drive strong GUS expression in the whole plant. In the virus infection tests, the GUS activity was strongly induced in PN4-GUS transgenic plants after being challenged with potexviruses. Infiltration of the transgenic plants individually with BaMV coat protein (CP) or triple gene block protein 1 (TGBp1) revealed that only TGBp1 was crucial for inducing the NbAGO5 promoter. To identify the factors responsible for controlling the activity of the NbAGO5 promoter, we employed yeast one-hybrid screening on a transcription factor cDNA library. The result showed that NbNAC42 and NbZFP3 could directly bind the 704 bp promoter regions of NbAGO5. By using overexpressing and virus-induced gene silencing techniques, we found that NbNAC42 and NbZFP3 regulated and downregulated, respectively, the expression of the NbAGO5 gene. Upon virus infection, NbNAC42 played an important role in regulating the expression of NbAGO5. Together, these results provide new insights into the modulation of the defense mechanism of N. benthamiana against viruses. This virus inducible promoter could be an ideal candidate to drive the target gene expression that could improve the anti-virus abilities of crops in the future.

Genome-wide analysis of the C2H2 zinc finger protein gene family and its response to salt stress in ginseng, Panax ginseng Meyer

The C2H2 zinc finger protein (C2H2-ZFP) gene family plays important roles in response to environmental stresses and several other biological processes in plants. Ginseng is a precious medicinal herb cultivated in Asia and North America. However, little is known about the C2H2-ZFP gene family and its functions in ginseng. Here, we identified 115 C2H2-ZFP genes from ginseng, defined as the PgZFP gene family. It was clustered into five groups and featured with eight conserved motifs, with each gene containing one to six of them. The family genes are categorized into 17 gene ontology subcategories and have numerous regulatory elements responsive to a variety of biological process, suggesting their functional differentiation. The 115 PgZFP genes were spliced into 228 transcripts at seed setting stage and varied dramatically in expression across tissues, developmental stages, and genotypes, but they form a co-expression network, suggesting their functional correlation. Furthermore, four genes, PgZFP31, PgZFP78-01, PgZFP38, and PgZFP39-01, were identified from the gene family that were actively involved in plant response to salt stress. These results provide new knowledge on origin, differentiation, evolution, and function of the PgZFP gene family and new gene resources for C2H2-ZFP gene research and application in ginseng and other plant species.

Mining Beneficial Genes for Salt Tolerance From a Core Collection of Rice Landraces at the Seedling Stage Through Genome-Wide Association Mapping

Rice is a salt-sensitive plant. High concentration of salt will hinder the absorption of water and nutrients and ultimately affect the yield. In this study, eight seedling-stage salt-related traits within a core collection of rice landraces were evaluated under salinity stress (100 mM NaCl) and normal conditions in a growth chamber. Genome-wide association study (GWAS) was performed with the genotypic data including 2,487,353 single-nucleotide polymorphisms (SNPs) detected in the core collection. A total of 65 QTLs significantly associated with salt tolerance (ST) were identified by GWAS. Among them, a co-localization QTL qTL4 associated with the SKC, RN/K, and SNC on chromosome 6, which explained 14.38-17.94% of phenotypic variation, was selected for further analysis. According to haplotype analysis, qRT-PCR analysis, and sequence alignment, it was finally determined that 4 candidate genes (LOC_Os06g47720, LOC_Os06g47820, LOC_Os06g47850, LOC_Os06g47970) were related to ST. The results provide useful candidate genes for marker assisted selection for ST in the rice molecular breeding programs.

Innovation and Emerging Roles of Populus trichocarpa TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR Transcription Factors in Abiotic Stresses by Whole-Genome Duplication

The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) family proteins are plant-specific transcription factors that have been well-acknowledged for designing the architectures of plant branch, shoot, and inflorescence. However, evidence for their innovation and emerging role in abiotic stress has been lacking. In this study, we identified a total of 36 TCP genes in Populus trichocarpa, 50% more than that in Arabidopsis (i.e., 24). Comparative intra-genomes showed that such significant innovation was mainly due to the most recent whole genome duplication (rWGD) in Populus lineage around Cretaceous-Paleogene (K-Pg) boundary after the divergence from Arabidopsis. Transcriptome analysis showed that the expressions of PtrTCP genes varied among leaf, stem, and root, and they could also be elaborately regulated by abiotic stresses (e.g., cold and salt). Moreover, co-expression network identified a cold-associated regulatory module including PtrTCP31, PtrTCP10, and PtrTCP36. Of them, PtrTCP10 was rWGD-duplicated from PtrTCP31 and evolved a strong capability of cold induction, which might suggest a neofunctionalization of PtrTCP genes and contribute to the adaptation of Populus lineage during the Cenozoic global cooling. Evidentially, overexpression of PtrTCP10 into Arabidopsis increased freezing tolerance and salt susceptibility. Integrating co-expression network and cis-regulatory element analysis confirmed that PtrTCP10 can regulate the well-known cold- and salt-relevant genes (e.g., ZAT10, GolS2, and SOS1), proving that PtrTCP10 is an evolutionary innovation in P. trichocarpa response to environmental changes. Altogether, our results provide evidence of the rWGD in P. trichocarpa responsible for the innovation of PtrTCP genes and their emerging roles in environmental stresses.

Innovation and Emerging Roles of Populus trichocarpa TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR Transcription Factors in Abiotic Stresses by Whole-Genome Duplication

The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) family proteins are plant-specific transcription factors that have been well-acknowledged for designing the architectures of plant branch, shoot, and inflorescence. However, evidence for their innovation and emerging role in abiotic stress has been lacking. In this study, we identified a total of 36 TCP genes in Populus trichocarpa, 50% more than that in Arabidopsis (i.e., 24). Comparative intra-genomes showed that such significant innovation was mainly due to the most recent whole genome duplication (rWGD) in Populus lineage around Cretaceous-Paleogene (K-Pg) boundary after the divergence from Arabidopsis. Transcriptome analysis showed that the expressions of PtrTCP genes varied among leaf, stem, and root, and they could also be elaborately regulated by abiotic stresses (e.g., cold and salt). Moreover, co-expression network identified a cold-associated regulatory module including PtrTCP31, PtrTCP10, and PtrTCP36. Of them, PtrTCP10 was rWGD-duplicated from PtrTCP31 and evolved a strong capability of cold induction, which might suggest a neofunctionalization of PtrTCP genes and contribute to the adaptation of Populus lineage during the Cenozoic global cooling. Evidentially, overexpression of PtrTCP10 into Arabidopsis increased freezing tolerance and salt susceptibility. Integrating co-expression network and cis-regulatory element analysis confirmed that PtrTCP10 can regulate the well-known cold- and salt-relevant genes (e.g., ZAT10, GolS2, and SOS1), proving that PtrTCP10 is an evolutionary innovation in P. trichocarpa response to environmental changes. Altogether, our results provide evidence of the rWGD in P. trichocarpa responsible for the innovation of PtrTCP genes and their emerging roles in environmental stresses.

The spinach YY genome reveals sex chromosome evolution, domestication, and introgression history of the species

Background

Spinach (Spinacia oleracea L.) is a dioecious species with an XY sex chromosome system, but its Y chromosome has not been fully characterized. Our knowledge about the history of its domestication and improvement remains limited.

Results

A high-quality YY genome of spinach is assembled into 952 Mb in six pseudo-chromosomes. By a combination of genetic mapping, Genome-Wide Association Studies, and genomic analysis, we characterize a 17.42-Mb sex determination region (SDR) on chromosome 1. The sex chromosomes of spinach evolved when an insertion containing sex determination genes occurred, followed by a large genomic inversion about 1.98 Mya. A subsequent burst of SDR-specific repeats (0.1–0.15 Mya) explains the large size of this SDR. We identify a Y-specific gene, NRT1/PTR 6.4 which resides in this insertion, as a strong candidate for the sex determination or differentiation factor. Resequencing of 112 spinach genomes reveals a severe domestication bottleneck approximately 10.87 Kya, which dates the domestication of spinach 7000 years earlier than the archeological record. We demonstrate that a strong selection signal associated with internode elongation and leaf area expansion is associated with domestication of edibility traits in spinach. We find that several strong genomic introgressions from the wild species Spinacia turkestanica and Spinacia tetrandra harbor desirable alleles of genes related to downy mildew resistance, frost resistance, leaf morphology, and flowering-time shift, which likely contribute to spinach improvement.

Conclusions

Analysis of the YY genome uncovers evolutionary forces shaping nascent sex chromosome evolution in spinach. Our findings provide novel insights about the domestication and improvement of spinach.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-022-02633-x.

C2H2 Zinc Finger Proteins Response to Abiotic Stress in Plants

Abiotic stresses have already exhibited the negative effects on crop growth and development, thereby influencing crop quality and yield. Therefore, plants have developed regulatory mechanisms to adopt against such harsh changing environmental conditions. Recent studies have shown that zinc finger protein transcription factors play a crucial role in plant growth and development as well as in stress response. C2H2 zinc finger proteins are one of the best-studied types and have been shown to play diverse roles in the plant abiotic stress responses. However, the C2H2 zinc finger network in plants is complex and needs to be further studied in abiotic stress responses. Here in this review, we mainly focus on recent findings on the regulatory mechanisms, summarize the structural and functional characterization of C2H2 zinc finger proteins, and discuss the C2H2 zinc finger proteins involved in the different signal pathways in plant responses to abiotic stress.

Overexpression of MdZAT5, an C2H2-Type Zinc Finger Protein, Regulates Anthocyanin Accumulation and Salt Stress Response in Apple Calli and Arabidopsis

Zinc finger proteins are widely involved and play an important role in plant growth and abiotic stress. In this research, MdZAT5, a gene encoding C2H2-type zinc finger protein, was cloned and investigated. The MdZAT5 was highly expressed in flower tissues by qRT-PCR analyses and GUS staining. Promoter analysis showed that MdZAT5 contained multiple response elements, and the expression levels of MdZAT5 were induced by various abiotic stress treatments. Overexpression of MdZAT5 in apple calli positively regulated anthocyanin accumulation by activating the expressions of anthocyanin biosynthesis-related genes. Overexpression of MdZAT5 in Arabidopsis also enhanced the accumulation of anthocyanin. In addition, MdZAT5 increased the sensitivity to salt stress in apple calli. Ectopic expression of MdZAT5 in Arabidopsis reduced the expression of salt-stress-related genes (AtNHX1 and AtABI1) and improved the sensitivity to salt stress. In conclusion, these results suggest that MdZAT5 plays a positive regulatory role in anthocyanin accumulation and negatively regulates salt resistance.

Genome-Wide Identification of the Q-type C2H2 Transcription Factor Family in Alfalfa (Medicago sativa) and Expression Analysis under Different Abiotic Stresses

Q-type C2H2 zinc-finger protein (C2H2-ZFP) transcription factors are associated with many plant growth development and environmental stress responses. To date, there have been few analyses of the Q-type C2H2-ZFP gene family in alfalfa (Medicago sativa subsp. sativa). In this study, we identified 58 Q-type C2H2-ZFPs across the entire alfalfa genome, and the gene structure, motif composition, chromosomal mapping, and cis-regulatory elements were explored, as well as the expression profiles of specific tissues and the response under different abiotic stresses. According to their phylogenetic features, these 58 MsZFPs were divided into 12 subgroups. Synteny analysis showed that duplication events play a vital role in the expansion of the MsZFP gene family. The collinearity results showed that a total of 26 and 42 of the 58 MsZFP genes were homologous with Arabidopsis and M. truncatula, respectively. The expression profiles showed that C2H2-ZFP genes played various roles in different tissues and abiotic stresses. The results of subsequent quantitative real-time polymerase chain reaction (qRT-PCR) showed that the nine selected MsZFP genes were rapidly induced under different abiotic stresses, indicating that C2H2-ZFP genes are closely related to abiotic stress. This study provides results on MsZFP genes, their response to various abiotic stresses, and new information on the C2H2 family in alfalfa.

In Silico Functional Prediction and Expression Analysis of C2H2 Zinc-Finger Family Transcription Factor Revealed Regulatory Role of ZmZFP126 in Maize Growth

The C2H2-zinc finger proteins (ZFP) comprise a large family of transcription factors with various functions in biological processes. In maize, the function regulation of C2H2- zine finger (ZF) genes are poorly understood. We conducted an evolution analysis and functional prediction of the maize C2H2-ZF gene family. Furthermore, the ZmZFP126 gene has been cloned and sequenced for further favorable allelic variation discovery. The phylogenetic analysis of the C2H2-ZF domain indicated that the position and sequence of the C2H2-ZF domain of the poly-zinc finger gene are relatively conserved during evolution, and the C2H2-ZF domain with the same position is highly conserved. The expression analysis of the C2H2-ZF gene family in 11 tissues at different growth stages of B73 inbred lines showed that genes with multiple transcripts were endowed with more functions. The expression analysis of the C2H2-ZF gene in P1 and P2 inbred lines under drought conditions showed that the C2H2-ZF genes were mainly subjected to negative regulation under drought stress. Functional prediction indicated that the maize C2H2-ZF gene is mainly involved in reproduction and development, especially concerning the formation of important agronomic traits in maize yield. Furthermore, sequencing and correlation analysis of the ZmZFP126 gene indicated that this gene was significantly associated with the SDW-NAP and TDW-NAP. The analysis of the relationship between maize C2H2-ZF genes and C2H2-ZF genes with known functions indicated that the functions of some C2H2-ZF genes are relatively conservative, and the functions of homologous genes in different species are similar.