LIP19, a basic region leucine zipper protein, is a Fos-like molecular switch in the cold signaling of rice plants

A novel wheat S1-bZIP gene, TabZIP11-D, confers stress resistance in Arabidopsis

Most subgroup S1 basic leucine zipper (bZIP) transcription factors (TFs) play a crucial role in the abiotic stress responses. However, their functions and molecular mechanisms remain poorly characterized in wheat (Triticum aestivum L.). In this study, we identified a novel subgroup S1 bZIP gene, designated TabZIP11-D, which was transcriptionally responsive to abscisic acid (ABA), salt, and cold stresses. TabZIP11-D encodes a nuclear-localized protein that lacks transcriptional activation activity in yeast. The Ca2+ blocker LaCl3 significantly suppressed the salt-induced expression of TabZIP11-D. TabZIP11-D interacted with the Ca2+-dependent protein kinases (TaCDPK1, TaCDPK5, TaCDPK9-1, and TaCDPK30) and the CBL-interacting protein kinase TaCIPK31. Overexpression of TabZIP11-D enhanced salt and freezing tolerance by modulating soluble sugar and proline accumulation, reducing hydrogen peroxide (H2O2) and malondialdehyde (MDA) contents, and regulating the expression levels of stress-responsive genes. Furthermore, TabZIP11-D formed a homodimer with itself and heterodimers with group C bZIP proteins. Modified yeast one-hybrid assays revealed that TabZIP14 and TabZIP36 significantly enhanced TabZIP11-D binding to the G-box cis-element in the promoter region of TaCBF1 gene. These findings demonstrate that TabZIP11-D heterodimerizes with TabZIP14/36 to regulate cold signaling by promoting the TaCBF1 transcription. TabZIP11-D functions as a positive regulator in the salt stress response by interacting with TaCDPK1/5/9-1/30 and TaCIPK31.

Overexpression of the Transcription Factor GmbZIP60 Increases Salt and Drought Tolerance in Soybean (Glycine max)

The regulation of downstream responsive genes by transcription factors (TFs) is a critical step in the stress response system of plants. While bZIP transcription factors are known to play important roles in stress reactions, their functional characterization in soybeans remains limited. Here, we identified a soybean bZIP gene, GmbZIP60, which encodes a protein containing a typical bZIP domain with a basic region and a leucine zipper region. Subcellular localization studies confirmed that GmbZIP60 is localized in the nucleus. Expression analysis demonstrated that GmbZIP60 is induced by salt stress, drought stress, and various plant hormone treatments, including abscisic acid (ABA), ethylene (ETH), and methyl jasmonate acid (MeJA). Overexpressing GmbZIP60 (OE-GmbZIP60) in transgenic soybean and rice enhanced tolerance to both salt and drought stresses. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis indicated that the expression levels of abiotic stress-responsive genes were significantly higher in transgenic plants than in wild-type (WT) plants under stress conditions. Chromatin immunoprecipitation-qPCR (ChIP-qPCR) analysis further confirmed that GmbZIP60 directly binds to the promoters of abiotic stress-related genes induced by ABA, ETH, JA, and salicylic acid (SA). Overall, these findings revealed GmbZIP60 as a positive regulator of salt and drought stress tolerance.

Plant Coping with Cold Stress: Molecular and Physiological Adaptive Mechanisms with Future Perspectives

Cold stress strongly hinders plant growth and development. However, the molecular and physiological adaptive mechanisms of cold stress tolerance in plants are not well understood. Plants adopt several morpho-physiological changes to withstand cold stress. Plants have evolved various strategies to cope with cold stress. These strategies included changes in cellular membranes and chloroplast structure, regulating cold signals related to phytohormones and plant growth regulators (ABA, JA, GA, IAA, SA, BR, ET, CTK, and MET), reactive oxygen species (ROS), protein kinases, and inorganic ions. This review summarizes the mechanisms of how plants respond to cold stress, covering four main signal transduction pathways, including the abscisic acid (ABA) signal transduction pathway, Ca2+ signal transduction pathway, ROS signal transduction pathway, and mitogen-activated protein kinase (MAPK/MPK) cascade pathway. Some transcription factors, such as AP2/ERF, MYB, WRKY, NAC, and bZIP, not only act as calmodulin-binding proteins during cold perception but can also play important roles in the downstream chilling-signaling pathway. This review also highlights the analysis of those transcription factors such as bHLH, especially bHLH-type transcription factors ICE, and discusses their functions as phytohormone-responsive elements binding proteins in the promoter region under cold stress. In addition, a theoretical framework outlining plant responses to cold stress tolerance has been proposed. This theory aims to guide future research directions and inform agricultural production practices, ultimately enhancing crop resilience to cold stress.

WD40 protein OsTTG1 promotes anthocyanin accumulation and CBF transcription factor-dependent pathways for rice cold tolerance

Temperature is a critical abiotic factor affecting rice (Oryza sativa L.) yields, and cold stress at the seedling stage can inhibit plant growth or even be fatal. Antioxidants such as anthocyanins accumulate in a variety of plants during cold stress, but the underlying mechanisms are not well understood. Here, we report that rice TRANSPARENT TESTA GLABRA 1 (OsTTG1), a major regulator of anthocyanin biosynthesis in rice, responds to short- and long-term cold stress at both the transcriptional and protein levels. Metabolomic and transcriptomic data indicate that OsTTG1 activates the expression of anthocyanidin synthase (OsANS) genes under cold stress. Our data also suggest that OsTTG1 forms a MYB-bHLH-WD (MBW) complex with Basic helix-loop-helix 148 (OsbHLH148) and Myb-related S3 (OsMYBS3), and this complex activates the expression of Dehydration-responsive element-binding protein 1 (OsDREB1) and OsANS genes. Together, our findings reveal the mechanisms by which OsTTG1 coordinates both anthocyanin biosynthesis and the expression of cold-responsive genes in colored rice, providing genetic resources for future cold resistance breeding in rice.

TaFAR9 and TaFAR10 synergistically regulate fertility conversion of photo-thermo-sensitive genic male sterility lines in wheat by modulating ROS homeostasis

Photo-thermo-sensitive genic male sterility (PTGMS), which exhibits varying fertility levels under different environmental conditions, is a crucial method for heterosis utilization in wheat. However, the mechanisms underlying fertility conversion remain unclear. In the study, three BS type PTGMS lines were analyzed to study fertility conversion characteristics. The results indicated that the fertility conversion occurred during meiosis and was accompanied by an increase in reactive oxygen species (ROS) under a sterile environment. TaFAR9 encoding a novel fatty acyl CoA reductase was identified using transcriptome sequencing. Expression analysis suggested that TaFAR9 was localized in the endoplasmic reticulum (ER), with high expression levels in anthers. Furthermore, the down-regulation of TaFAR9 expression displayed characteristics of male sterility, accompanied by the accumulation of ROS. Cytological analysis revealed abnormal development in the anther and pollen walls of TaFAR9-silenced lines. Additionally, TaFAR9 and TaFAR10 were confirmed to physically interact using molecular docking simulation, yeast two-hybrid, luciferase complementation, and bimolecular fluorescence complementation assays. The reduced expression of TaFAR10 also exhibited male sterility and ROS burst. Moreover, the co-silencing of TaFAR9 and TaFAR10 produced sterility phenotypes that were similar to those observed when silencing TaFAR9 or TaFAR10 individually. Transcriptome analysis suggested that the ROS burst in BSMV: TaFAR9/10 anthers can result in cellular metabolic disorders. These findings indicate that TaFAR9 and TaFAR10 may form heterodimers that synergistically regulate fertility conversion in PTGMS lines by modulating ROS metabolism. And this study offers a fresh insight into the regulatory processes involved in fertility conversion in PTGMS lines.

A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice

Transposable elements (TEs) are ubiquitous genomic components and hard to study due to being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing data. Coupling the 232 genomes with 15 existing assemblies, we developed a pan-TE map comprising both cultivated and wild Asian rice. We detected 177 084 high-quality TE variations and inferred their derived state using outgroups. We found TEs were one source of phenotypic variation during rice domestication and differentiation. We identified 1246 genes whose expression variation was associated with TEs but not single-nucleotide polymorphisms (SNPs), such as OsRbohB, and validated OsRbohB's relative expression activity using a dual-Luciferase (LUC) reporter assays system. Our pan-TE map allowed us to detect multiple novel loci associated with agronomic traits. Collectively, our findings highlight the contributions of TEs to domestication, differentiation and agronomic traits in rice, and there is massive potential for gene cloning and molecular breeding by the high-quality Asian pan-TE map we generated.

OsbZIP38/87-mediated activation of OsHXK7 improves the viability of rice cells under hypoxic conditions

Maintenance of energy metabolism is critical for rice (Oryza sativa) tolerance under submerged cultivation. Here, OsHXK7 was the most actively induced hexokinase gene in the embryos of hypoxically germinating rice seeds. Suspension-cultured cells established from seeds of T-DNA null mutants for the OsHXK7 locus did not regrow after 3-d-hypoxic stress and showed increased susceptibility to low-oxygen stress-in terms of viability-and decreased alcoholic fermentation activities compared to those of the wild-type. The promoter element containing the TGACG-motif, a well-known target site for the basic leucine zipper (bZIP) transcription factors, was responsible for sugar regulation of the OsHXK7 promoter activity. Systematic screening of the OsbZIP genes showing the similar expression patterns to that of OsHXK7 in the transcriptomic datasets produced two bZIP genes, OsbZIP38 and 87, belonging to the S1 bZIP subfamily as the candidate for the activator for this gene expression. Gain- and loss-of-function experiments through transient expression assays have demonstrated that these two bZIP proteins are indeed involved in the induction of OsHXK7 expression under starvation or low-energy conditions. Our finding suggests that C/S1 bZIP network-mediated hypoxic deregulation of sugar-responsive genes may work in concert for the molecular adaptation of rice cells to submergence.

Identification and Functional Characterization of Two Major Loci Associated with Resistance against Brown Planthoppers (Nilaparvata lugens (Stål)) Derived from Oryza nivara

The brown planthopper (BPH) is a highly destructive pest of rice, causing significant economic losses in various regions of South and Southeast Asia. Researchers have made promising strides in developing resistance against BPH in rice. Introgression line RPBio4918-230S, derived from Oryza nivara, has shown consistent resistance to BPH at both the seedling and adult stages of rice plants. Segregation analysis has revealed that this resistance is governed by two recessive loci, known as bph39(t) and bph40(t), contributing to 21% and 22% of the phenotypic variance, respectively. We later mapped the genes using a backcross population derived from a cross between Swarna and RPBio4918-230S. We identified specific marker loci, namely RM8213, RM5953, and R4M17, on chromosome 4, flanking the bph39(t) and bph40(t) loci. Furthermore, quantitative expression analysis of candidate genes situated between the RM8213 and R4M17 markers was conducted. It was observed that eight genes exhibited up-regulation in RPBio4918-230S and down-regulation in Swarna after BPH infestation. One gene of particular interest, a serine/threonine-protein kinase receptor (STPKR), showed significant up-regulation in RPBio4918-230S. In-depth sequencing of the susceptible and resistant alleles of STPKR from Swarna and RPBio4918-230S, respectively, revealed numerous single nucleotide polymorphisms (SNPs) and insertion-deletion (InDel) mutations, both in the coding and regulatory regions of the gene. Notably, six of these mutations resulted in amino acid substitutions in the coding region of STPKR (R5K, I38L, S120N, T319A, T320S, and F348S) when compared to Swarna and the reference sequence of Nipponbare. Further validation of these mutations in a set of highly resistant and susceptible backcross inbred lines confirmed the candidacy of the STPKR gene with respect to BPH resistance controlled by bph39(t) and bph40(t). Functional markers specific for STPKR have been developed and validated and can be used for accelerated transfer of the resistant locus to elite rice cultivars.

Insight into the bZIP gene family in Lagenaria siceraria: Genome and transcriptome analysis to understand gene diversification in Cucurbitaceae and the roles of LsbZIP gene expression and function under cold stress

The basic leucine zipper (bZIP) as a well-known transcription factor family, figures prominently in diverse biological and developmental processes and response to abiotic/biotic stresses. However, no knowledge of the bZIP family is available for the important edible Cucurbitaceae crop bottle gourd. Herein, we identified 65 putative LsbZIP genes and characterized their gene structure, phylogenetic and orthologous relationships, gene expression profiles in different tissues and cultivars, and responsive genes under cold stress. The phylogenetic tree of 16 released Cucurbitaceae plant genomes revealed the evolutionary convergence and divergence of bZIP family. Based on the specific domains, LsbZIP family were classified into 12 clades (A-K, S) with similar motifs and exon-intron distribution. 65 LsbZIP genes have undergone 19 segmental and two tandem duplication events with purifying selection. The expression profiling of LsbZIP genes showed tissue-specific but no cultivar-specific pattern. The cold stress-responsive candidate LsbZIP genes were analyzed and validated by RNA-Seq and RT-PCR, providing new insights of transcriptional regulation of bZIP family genes in bottle gourd and their potential functions in cold-tolerant variety breeding.

Characterization and expression analysis of basic leucine zipper (bZIP) transcription factors responsive to chilling injury in peach fruit

BACKGROUND

Peach (Prunus persica L.) is prone to chilling injury as exhibited by inhibition of the ethylene production, failure in softening, and the manifestation of internal browning. The basic leucine zipper (bZIP) transcription factors play an essential role in regulatory networks that control many processes associated with physiological, abiotic and biotic stress responses in fruits. Formerly, the underlying molecular and regulatory mechanism of (bZIP) transcription factors responsive to chilling injury in peach fruit is still elusive.

METHODS AND RESULTS

In the current experiment, the solute peach 'Zhongyou Peach No. 13' was used as the test material and cold storage at low temperature (4 °C). It was found that long-term low-temperature storage induced the production of ethylene, the hardness of the pulp decreased, and the low temperature also induced ABA accumulation. The changes of ABA and ethylene in peach fruits during low-temperature storage were clarified. Since the bZIP transcription factor is involved in the regulation of downstream pathways of ABA signals, 47 peach bZIP transcription factor family genes were identified through bioinformatics analysis. Further based on RT-qPCR analysis, 18 PpbZIP genes were discovered to be expressed in refrigerated peach fruits. Among them, the expression of PpbZIP23 and PpbZIP25 was significantly reduced during the refrigeration process, the promoter analysis of these genes found that this region contains the MYC/MYB/ABRES binding element, but not the DRES/CBFS element, indicating that the expression may be regulated by the ABA-dependent cold induction pathway, thereby responding to chilling injury in peach fruit.

CONCLUSIONS

Over investigation will provide new insights for further postharvest protocols related to molecular changes during cold storage and will prove a better cope for chilling injury.

GmbZIP152, a Soybean bZIP Transcription Factor, Confers Multiple Biotic and Abiotic Stress Responses in Plant

Soybean is one of the most important food crops in the world. However, with the environmental change in recent years, many environmental factors like drought, salinity, heavy metal, and disease seriously affected the growth and development of soybean, causing substantial economic losses. In this study, we screened a bZIP transcription factor gene, GmbZIP152, which is significantly induced by Sclerotinia sclerotiorum (S. sclerotiorum), phytohormones, salt-, drought-, and heavy metal stresses in soybean. We found that overexpression of GmbZIP152 in Arabidopsis (OE-GmbZIP152) enhances the resistance to S. sclerotiorum and the tolerance of salt, drought, and heavy metal stresses compared to wild-type (WT). The antioxidant enzyme related genes (including AtCAT1, AtSOD, and AtPOD1) and their enzyme activities are induced by S. sclerotiorum, salt, drought, and heavy metal stress in OE-GmbZIP152 compared to WT. Furthermore, we also found that the expression level of biotic- and abiotic-related marker genes (AtLOX6, AtACS6, AtERF1, and AtABI2, etc.) were increased in OE-GmbZIP152 compared to WT under S. sclerotiorum and abiotic stresses. Moreover, we performed a Chromatin immunoprecipitation (ChIP) assay and found that GmbZIP152 could directly bind to promoters of ABA-, JA-, ETH-, and SA-induced biotic- and abiotic-related genes in soybean. Altogether, GmbZIP152 plays an essential role in soybean response to biotic and abiotic stresses.

bZIP71 delays flowering by suppressing Ehd1 expression in rice

Flowering time is a fundamental factor determining the global distribution and final yield of rice (Oryza sativa). Although diverse flowering time genes have been reported in this crop, the transcriptional regulation of its key flowering genes are poorly understood. Here, we report that a basic leucine zipper transcription factor, bZIP71, functions as a flowering repressor. The overexpression of bZIP71 delays flowering, while the bzip71 mutant flowers early in both long-day and short-day conditions. A genetic analysis showed that the regulation of flowering by bZIP71 might be independent of Heading date 2 (Hd2), Hd4, and Hd5. Importantly, bZIP71 directly associates with the Early heading date 1 (Ehd1) promoter and represses its transcription, and genetically the function of bZIP71 is impaired in the ehd1 mutant. Moreover, bZIP71 interacts with major components of polycomb repressive complex 2 (PRC2), SET domain group protein 711 (SDG711), and Fertilization independent endosperm 2 (FIE2), through which bZIP71 regulates the H3K27me3 level of Ehd1. Taken together, we present a transcriptional regulatory mechanism in which bZIP71 enhances the H3K27me3 level of Ehd1 and transcriptionally represses its expression, which not only offers a novel insight into a flowering pathway, but also provides a valuable putative target for the genetic engineering and breeding of elite rice cultivars.

Wheat ocs-Element Binding Factor 1 Enhances Thermotolerance by Modulating the Heat Stress Response Pathway

The basic leucine zipper family (bZIP) represents one of the largest families of transcription factors that play an important role in plant responses to abiotic stresses. However, their role in contributing to thermotolerance in plants is not well explored. In this article, two homoeologs of wheat ocs-element binding factor 1 (TaOBF1-5B and TaOBF1-5D) were found to be heat-responsive TabZIP members. Their expression analysis in Indian wheat cultivars revealed their differential expression pattern and TaOBF1-5B was found to be more receptive to heat stress. Consistent with this, the heterologous overexpression of TaOBF1-5B in Arabidopsis thaliana and Oryza sativa promoted the expression of stress-responsive genes, which contributed to thermotolerance in transgenic plants. TaOBF1-5B was seen to interact with TaHSP90 in the nucleus and TaSTI in the nucleolus and the ER. Thus, the results suggest that TaOBF1-5B might play an important regulatory role in the heat stress response and is a major factor governing thermotolerance in plants.

DgbZIP3 interacts with DgbZIP2 to increase the expression of DgPOD for cold stress tolerance in chrysanthemum

The bZIP transcription factor plays a very important role in abiotic stresses, e.g. drought, salt, and low-temperature stress, but the mechanism of action at low temperature is still unclear. In this study, overexpression of DgbZIP3 led to increased tolerance of chrysanthemum (Chrysanthemum morifolium Ramat.) to cold stress, whereas antisense suppression of DgbZIP3 resulted in decreased tolerance. Electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation (ChIP), luciferase complementary imaging analysis (LCI), and dual-luciferase reporter gene detection (DLA) experiments indicated that DgbZIP3 directly bound to the promoter of DgPOD and activated its expression. DgbZIP2 was identified as a DgbZIP3-interacting protein using yeast two-hybrid, co-immunoprecipitation, LCI, and bimolecular fluorescence complementation assays. Overexpression of DgbZIP2 led to increased tolerance of chrysanthemum to cold stress, whereas antisense suppression of DgbZIP2 resulted in decreased tolerance. A ChIP-qPCR experiment showed that DgbZIP2 was highly enriched in the promoter of DgPOD, while DLA, EMSA, and LCI experiments further showed that DgbZIP2 could not directly regulate the expression of DgPOD. The above results show that DgbZIP3 interacts with DgbZIP2 to regulate the expression of DgPOD to promote an increase in peroxidase activity, thereby regulating the balance of reactive oxygen species and improving the tolerance of chrysanthemum to low-temperature stress.

The bZIP Transcription Factor Family in Adzuki Bean (Vigna Angularis): Genome-Wide Identification, Evolution, and Expression Under Abiotic Stress During the Bud Stage

Adzuki bean (Vigna angularis) is an important dietary legume crop that was first cultivated and domesticated in Asia. Currently, little is known concerning the evolution and expression patterns of the basic leucine zipper (bZIP) family transcription factors in the adzuki bean. Through the PFAM search, 72 bZIP members of adzuki bean (VabZIP) were identified from the reference genome. Most of them were located on 11 chromosomes and seven on an unknown chromosome. A comprehensive analysis, including evolutionary, motifs, gene structure, cis-elements, and collinearity was performed to identify VabZIP members. The subcellular localization results showed VabZIPs might locate on the nuclear. Quantitative real-time PCR (qRT-PCR) analysis of the relative expression of VabZIPs in different tissues at the bud stage revealed that VabZIPs had a tissue-specific expression pattern, and its expression was influenced by abiotic stress. These characteristics of VabZIPs provide insights for future research aimed at developing interventions to improve abiotic stress resistance.

OsbZIP18, a Positive Regulator of Serotonin Biosynthesis, Negatively Controls the UV-B Tolerance in Rice

Serotonin (5-hydroxytryptamine) plays an important role in many developmental processes and biotic/abiotic stress responses in plants. Although serotonin biosynthetic pathways in plants have been uncovered, knowledge of the mechanisms of serotonin accumulation is still limited, and no regulators have been identified to date. Here, we identified the basic leucine zipper transcription factor OsbZIP18 as a positive regulator of serotonin biosynthesis in rice. Overexpression of OsbZIP18 strongly induced the levels of serotonin and its early precursors (tryptophan and tryptamine), resulting in stunted growth and dark-brown phenotypes. A function analysis showed that OsbZIP18 activated serotonin biosynthesis genes (including tryptophan decarboxylase 1 (OsTDC1), tryptophan decarboxylase 3 (OsTDC3), and tryptamine 5-hydroxylase (OsT5H)) by directly binding to the ACE-containing or G-box cis-elements in their promoters. Furthermore, we demonstrated that OsbZIP18 is induced by UV-B stress, and experiments using UV-B radiation showed that transgenic plants overexpressing OsbZIP18 exhibited UV-B stress-sensitive phenotypes. Besides, exogenous serotonin significantly exacerbates UV-B stress of OsbZIP18_OE plants, suggesting that the excessive accumulation of serotonin may be responsible for the sensitivity of OsbZIP18_OE plants to UV-B stress. Overall, we identified a positive regulator of serotonin biosynthesis and demonstrated that UV-B-stress induced serotonin accumulation, partly in an OsbZIP18-dependent manner.

Identification of bZIP transcription factors and their responses to brown spot in pear

Basic leucine zipper (bZIP) is a conserved transcription factor (TF) widely present in eukaryotes, and it plays an important role in regulating plant growth and stress responses. To better understand the white pear bZIP gene family, comprehensive bioinformatics analysis of the pear genome was performed. A total of 84 PbbZIP genes were identified, which were divided into 13 subfamilies by phylogenetic analysis. The 84 PbbZIP genes were all located in the nucleus, and 77 of those genes were unevenly distributed across the 17 chromosomes of white pear. The other 7 PbbZIP genes were located on the scaffold. Subsequent expression profile analysis showed that PbbZIP genes in exocarp were significantly upregulated or downregulated in ‘Huangguan’ pear with brown spot (BS) compared with healthy pear and in response to hormonal treatment with gibberellin A₃ (GA₃). These results provide helpful insights into the characteristics of PbbZIP genes and their responses to BS in ‘Huangguan’ pear.

S1-bZIP Transcription Factors Play Important Roles in the Regulation of Fruit Quality and Stress Response

Sugar metabolism not only determines fruit sweetness and quality but also acts as signaling molecules to substantially connect with other primary metabolic processes and, therefore, modulates plant growth and development, fruit ripening, and stress response. The basic region/leucine zipper motif (bZIP) transcription factor family is ubiquitous in eukaryotes and plays a diverse array of biological functions in plants. Among the bZIP family members, the smallest bZIP subgroup, S1-bZIP, is a unique one, due to the conserved upstream open reading frames (uORFs) in the 5' leader region of their mRNA. The translated small peptides from these uORFs are suggested to mediate Sucrose-Induced Repression of Translation (SIRT), an important mechanism to maintain sucrose homeostasis in plants. Here, we review recent research on the evolution, sequence features, and biological functions of this bZIP subgroup. S1-bZIPs play important roles in fruit quality, abiotic and biotic stress responses, plant growth and development, and other metabolite biosynthesis by acting as signaling hubs through dimerization with the subgroup C-bZIPs and other cofactors like SnRK1 to coordinate the expression of downstream genes. Direction for further research and genetic engineering of S1-bZIPs in plants is suggested for the improvement of quality and safety traits of fruit.

Genome-wide identification and characterization of bZIP transcription factors and their expression profile under abiotic stresses in Chinese pear (Pyrus bretschneideri)

BACKGROUND

In plants, basic leucine zipper transcription factors (TFs) play important roles in multiple biological processes such as anthesis, fruit growth & development and stress responses. However, systematic investigation and characterization of bZIP-TFs remain unclear in Chinese white pear. Chinese white pear is a fruit crop that has important nutritional and medicinal values.

RESULTS

In this study, 62 bZIP genes were comprehensively identified from Chinese Pear, and 54 genes were distributed among 17 chromosomes. Frequent whole-genome duplication (WGD) and dispersed duplication (DSD) were the major driving forces underlying the bZIP gene family in Chinese white pear. bZIP-TFs are classified into 13 subfamilies according to the phylogenetic tree. Subsequently, purifying selection plays an important role in the evolution process of PbbZIPs. Synteny analysis of bZIP genes revealed that 196 orthologous gene pairs were identified between Pyrus bretschneideri, Fragaria vesca, Prunus mume, and Prunus persica. Moreover, cis-elements that respond to various stresses and hormones were found on the promoter regions of PbbZIP, which were induced by stimuli. Gene structure (intron/exon) and different compositions of motifs revealed that functional divergence among subfamilies. Expression pattern of PbbZIP genes differential expressed under hormonal treatment abscisic acid, salicylic acid, and methyl jasmonate  in pear fruits by real-time qRT-PCR.

CONCLUSIONS

Collectively, a systematic analysis of gene structure, motif composition, subcellular localization, synteny analysis, and calculation of synonymous (Ks) and non-synonymous (Ka) was performed in Chinese white pear. Sixty-two bZIP-TFs in Chinese pear were identified, and their expression profiles were comprehensively analyzed under ABA, SA, and MeJa hormones, which respond to multiple abiotic stresses and fruit growth and development. PbbZIP gene occurred through Whole-genome duplication and dispersed duplication events. These results provide a basic framework for further elucidating the biological function characterizations under multiple developmental stages and abiotic stress responses.

Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing

Background: As Oryza sativa ssp. indica and Oryza sativa ssp. japonica are the two major subspecies of Asian cultivated rice, the adaptative evolution of these varieties in divergent environments is an important topic in both theoretical and practical studies. However, the cell type-specific differentiation between indica and japonica rice varieties in response to divergent habitat environments, which facilitates an understanding of the genetic basis underlying differentiation and environmental adaptation between rice subspecies at the cellular level, is little known.

Methods: We analyzed a published single-cell RNA sequencing dataset to explore the differentially expressed genes between indica and japonica rice varieties in each cell type. To estimate the relationship between cell type-specific differentiation and environmental adaptation, we focused on genes in the WRKY, NAC, and BZIP transcription factor families, which are closely related to abiotic stress responses. In addition, we integrated five bulk RNA sequencing datasets obtained under conditions of abiotic stress, including cold, drought and salinity, in this study. Furthermore, we analyzed quiescent center cells in rice root tips based on orthologous markers in Arabidopsis.

Results: We found differentially expressed genes between indica and japonica rice varieties with cell type-specific patterns, which were enriched in the pathways related to root development and stress reposes. Some of these genes were members of the WRKY, NAC, and BZIP transcription factor families and were differentially expressed under cold, drought or salinity stress. In addition, LOC_Os01g16810, LOC_Os01g18670, LOC_Os04g52960, and LOC_Os08g09350 may be potential markers of quiescent center cells in rice root tips.

Conclusion: These results identified cell type-specific differentially expressed genes between indica-japonica rice varieties that were related to various environmental stresses and provided putative markers of quiescent center cells. This study provides new clues for understanding the development and physiology of plants during the process of adaptative divergence, in addition to identifying potential target genes for the improvement of stress tolerance in rice breeding applications.

OsGATA16, a GATA Transcription Factor, Confers Cold Tolerance by Repressing OsWRKY45-1 at the Seedling Stage in Rice

BACKGROUND

Cold stress is the main abiotic stress in rice, which seriously affects the growth and yield of rice. Identification of cold tolerance genes is of great significance for rice to solve these problems. GATA-family transcription factors involve diverse biological functions, however, their role in cold tolerance in rice remains unclear.

RESULTS

In this study, a GATA-type zinc finger transcription factor OsGATA16, which can improve cold tolerance, was isolated and characterized from rice. OsGATA16 belongs to OsGATA subfamily-II and contains 11 putative phosphorylation sites, a nuclear localization signal (NLS), and other several conserved domains. OsGATA16 was expressed in all plant tissues, with the strongest in panicles. It was induced by cold and ABA treatments, but was repressed by drought, cytokinin and JA, and acted as a transcriptional suppressor in the nucleus. Overexpression of OsGATA16 improves cold tolerance of rice at seedling stage. Under cold stress treatments, the transcription of four cold-related genes OsWRKY45-1, OsSRFP1, OsCYL4, and OsMYB30 was repressed in OsGATA16-overexpressing (OE) rice compared with wild-type (WT). Interestingly, OsGATA16 bound to the promoter of OsWRKY45-1 and repressed its expression. In addition, haplotype analysis showed that OsGATA16 polarized between the two major rice subspecies japonica and indica, and had a non-synonymous SNP8 (336^G) associated with cold tolerance.

CONCLUSION

OsGATA16 is a GATA transcription factor, which improves cold tolerance at seedling stage in rice. It acts as a positive regulator of cold tolerance by repressing some cold-related genes such as OsWRKY45-1, OsSRFP1, OsCYL4 and OsMYB30. Additionally, OsGATA16 has a non-synonymous SNP8 (336^G) associated with cold tolerance on CDS region. This study provides a theoretical basis for elucidating the mechanism of cold tolerance in rice and new germplasm resources for rice breeding.

Comparative analysis of the transcriptomes of two rice subspecies during domestication

Two subspecies of rice, Oryza sativa ssp. indica and O. sativa ssp. japonica, with reproductive isolation and differences in morphology and phenotypic differences, were established during the process of rice domestication. To understand how domestication has changed the transcriptomes of the two rice subspecies and given rise to the phenotypic differences, we obtained approximately 700 Gb RNA-Seq data from 26 indica and 25 japonica accessions, and identified 97,005 transcribed fragments and 4579 novel transcriptionally active regions. The two rice subspecies had significantly different gene expression profiles, we identified 1,357 (3.3% in all genes) differentially expressed genes (DEGs) between indica and japonica rice. Combining existing gene function studies, it is found that some of these differential genes are related to the differentiation of the two subspecies, such as grain shape and cold tolerance, etc. Functional annotation of these DEGs indicates that they are involved in cell wall biosynthesis and reproductive processes. Furthermore, compared with the non-DEGs, the DEGs from both subspecies had more 5'flanking regions with low polymorphism to divergence ratios, indicating a stronger positive selection pressure on the regulation of the DEGs. This study improves our understanding of the rice genome by comparatively analyzing the transcriptomes of indica and japonica rice and identifies DEGs those may be responsible for the reproductive isolation and phenotypic differences between the two rice subspecies.

Genome-wide identification and expression analysis of bZIP gene family in Carthamus tinctorius L

The basic leucine zipper (bZIP) is a widely known transcription factors family in eukaryotes. In plants, the role of bZIP proteins are crucial in various biological functions such as plant growth and development, seed maturation, response to light signal and environmental stress. To date, bZIP protein family has been comprehensively identified in Arabidopsis, castor, rice, ramie, soybean and other plant species, however, the complete genome-wide investigation of Carthamus tinctorius-bZIP family still remains unexplained. Here, we identified 52 putative bZIP genes from Carthamus tinctorius using a draft genome assembly and further analyzed their evolutionary classification, physicochemical properties, Conserved domain analysis, functional differentiation and the investigation of expression level in different tissues. Based on the common bZIP domain, CtbZIP family were clustered into 12 subfamilies renamed as (A-J, S, X), of which the X is a unique subfamily to Carthamus tinctorius. A total of 20 conserved protein motifs were found in CtbZIP proteins. The expression profiling of CtbZIP genes deciphered their tissue-specific pattern. Furthermore, the changes in CtbZIP transcript abundance suggested that their transcription regulation could be highly influenced by light intensity and hormones. Collectively, this study highlights all functional and regulatory elements of bZIP transcription factors family in Carthamus tinctorius which may serve as potential candidates for functional characterization in future.

Genome-wide analysis of the abiotic stress-related bZIP family in switchgrass

The large basic leucine zipper (bZIP) transcription factor family is conserved in plants. These proteins regulate growth, development, and stress response. Here, we conducted a genome-wide analysis to identify the bZIP genes associated with stress resistance in switchgrass (Panicum virgatum L.). We identified 178 PvbZIPs unevenly distributed on 18 switchgrass chromosomes. An evolutionary analysis segregated them into 10 subfamilies. Gene structure and conserved motif analyses indicated that the same subfamily members shared similar intron-exon modes and motif compositions. This finding corroborated the proposed PvbZIP family grouping. A promoter analysis showed that PvbZIP genes participate in various stress responses. Phylogenetic and synteny analyses characterized 111 switchgrass bZIPs as orthologs of 70 rice bZIPs. A protein interaction network analysis revealed that 22 proteins are involved in salt and drought tolerance. An expression atlas disclosed that the expression patterns of several PvbZIPs differ among various tissues and developmental stages. Online data demonstrated that 16 PvbZIPs were significantly downregulated and five were significantly upregulated in response to heat stress. Other PvbZIPs participated in responses to abiotic stress such as salt, drought, cold, and heat. Our genome-wide analysis and identification of the switchgrass bZIP family characterized multiple candidate PvbZIPs that regulate growth and stress response. This study lays theoretical and empirical foundations for future functional investigations into other transcription factors.

ABA-dependent bZIP transcription factor, CsbZIP18, from Camellia sinensis negatively regulates freezing tolerance in Arabidopsis

Overexpression of the tea plant gene CsbZIP18 in Arabidopsis impaired freezing tolerance, and CsbZIP18 is a negative regulator of ABA signaling and cold stress. Basic region/leucine zipper (bZIP) transcription factors play important roles in the abscisic acid (ABA) signaling pathway and abiotic stress response in plants. However, few bZIP transcription factors have been functionally characterized in tea plants (Camellia sinensis). In this study, a bZIP transcription factor, CsbZIP18, was found to be strongly induced by natural cold acclimation, and the expression level of CsbZIP18 was lower in cold-resistant cultivars than in cold-susceptible cultivars. Compared with wild-type (WT) plants, Arabidopsis plants constitutively overexpressing CsbZIP18 exhibited decreased sensitivity to ABA, increased levels of relative electrolyte leakage (REL) and reduced values of maximal quantum efficiency of photosystem II (F_v/F_m) under freezing conditions. The expression of ABA homeostasis- and signal transduction-related genes and abiotic stress-inducible genes, such as RD22, RD26 and RAB18, was suppressed in overexpression lines under freezing conditions. However, there was no significant change in the expression of genes involved in the C-repeat binding factor (CBF)-mediated ABA-independent pathway between WT and CsbZIP18 overexpression plants. These results indicate that CsbZIP18 is a negative regulator of freezing tolerance via an ABA-dependent pathway.

A genome-wide comparative analysis of bZIP transcription factors in G. arboreum and G. raimondii (Diploid ancestors of present-day cotton)

Basic leucine zipper motif (bZIP) transcription factors (TFs) are involved in plant growth regulation, development, and environmental stress responses. These genes have been well characterized in model plants. In current study, a genome-wide analysis of bZIP genes was performed in Gossypium raimondii and Gossypium arboreum taking Arabidopsis thaliana as a reference genome. In total, 85 members of G. raimondii and 87 members of G. arboreum were identified and designated as GrbZIPs and GabZIPs respectively. Phylogenetic analysis clustered bZIP genes into 11 subgroups (A, B, C, D, F, G, H, I, S and X). Gene structure analysis to find the intro-exon structures revealed 1-14 exons in both species. The maximum number of introns were present in subgroup G and D while genes in subgroup S were intron-less except GrbZIP78, which is a unique characteristic as compared to other groups. Results of motif analysis predicted that all three species share a common bZIP motif. A detailed comparison of bZIPs gene distribution on chromosomes has shown a diverse arrangement of genes in both cotton species. Moreover, the functional similarity with orthologs was also predicted. The findings of this study revealed close similarity in gene structure of both cotton species and diversity in gene distribution on chromosomes. This study supports the divergence of both species from the common ancestor and later diversity in gene distribution on chromosomes due to evolutionary changes. Additionally, this work will facilitate the functional characterization of bZIP genes in cotton. Outcomes of this study represent foundation research on the bZIP TFs family in cotton and as a reference for other crops.

Characterization of the bZIP Transcription Factor Family in Pepper (Capsicum annuum L.): CabZIP25 Positively Modulates the Salt Tolerance

The basic leucine zipper (bZIP) proteins compose a family of transcription factors (TFs), which play a crucial role in plant growth, development, and abiotic and biotic stress responses. However, no comprehensive analysis of bZIP family has been reported in pepper (Capsicum annuum L.). In this study, we identified and characterized 60 bZIP TF-encoding genes from two pepper genomes. These genes were divided into 10 groups based on their phylogenetic relationships with bZIP genes from Arabidopsis. Six introns/exons structural patterns within the basic and hinge regions and the conserved motifs were identified among all the pepper bZIP proteins, on the basis of which, we classify them into different subfamilies. Based on the transcriptomic data of Zunla-1 genome, expression analyses of 59 pepper bZIP genes (not including CabZIP25 of CM334 genome), indicated that the pepper bZIP genes were differentially expressed in the pepper tissues and developmental stages, and many of the pepper bZIP genes might be involved in responses to various abiotic stresses and phytohormones. Further, gene expression analysis, using quantitative real-time PCR (qRT-PCR), showed that the CabZIP25 gene was expressed at relatively higher levels in vegetative tissues, and was strongly induced by abiotic stresses and phytohormones. In comparing with wild type Arabidopsis, germination rate, fresh weight, chlorophyll content, and root lengths increased in the CabZIP25-overexpressing Arabidopsis under salt stress. Additionally, CabZIP25-silenced pepper showed lower chlorophyll content than the control plants under salt stress. These results suggested that CabZIP25 improved salt tolerance in plants. Taken together, our results provide new opportunities for the functional characterization of bZIP TFs in pepper.

The bZIP gene family in watermelon: genome-wide identification and expression analysis under cold stress and root-knot nematode infection

The basic leucine zipper (bZIP) family transcription factors play crucial roles in regulating plant development and stress response. In this study, we identified 62 ClabZIP genes from watermelon genome, which were unevenly distributed across the 11 chromosomes. These ClabZIP proteins could be classified into 13 groups based on the phylogenetic relationships, and members in the same group showed similar compositions of conserved motifs and gene structures. Transcriptome analysis revealed that a number of ClabZIP genes have important roles in the melatonin (MT) induction of cold tolerance. In addition, some ClabZIP genes were induced or repressed under red light (RL) or root-knot nematode infection according to the transcriptome data, and the expression patterns of several ClabZIP genes were further verified by quantitative real-time PCR, revealing their possible roles in RL induction of watermelon defense against nematode infection. Our results provide new insights into the functions of different ClabZIP genes in watermelon and their roles in response to cold stress and nematode infection.

Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

Background

The basic leucine zipper (bZIP) transcription factor is one of the most abundant and conserved transcription factor families. In addition to being involved in growth and development, bZIP transcription factors also play an important role in plant adaption to abiotic stresses.

Results

A total of 41 bZIP genes that encode 66 proteins were identified in Ipomoea trifida. They were distributed on 14 chromosomes of Ipomoea trifida. Segmental and tandem duplication analysis showed that segmental duplication played an important role in the ItfbZIP gene amplification. ItfbZIPs were divided into ten groups (A, B, C, D, E, F, G, H, I and S groups) according to their phylogenetic relationships with Solanum lycopersicum and Arabidopsis thaliana. The regularity of the exon/intron numbers and distributions is consistent with the group classification in evolutionary tree. Prediction of the cis-acting elements found that promoter regions of ItfbZIPs harbored several stress responsive cis-acting elements. Protein three-dimensional structural analysis indicated that ItfbZIP proteins mainly consisted of α-helices and random coils. The gene expression pattern from transcriptome data and qRT-PCR analysis showed that ItfbZIP genes expressed with a tissue-specific manner and differently expressed under various abiotic stresses, suggesting that the ItfbZIPs were involved in stress response and adaption in Ipomoea trifida.

Conclusions

Genome-wide identification, gene structure, phylogeny and expression analysis of bZIP gene in Ipomoea trifida supplied a solid theoretical foundation for the functional study of bZIP gene family and further facilitated the molecular breeding of sweet potato.

Electronic supplementary material

The online version of this article (10.1186/s12863-019-0743-y) contains supplementary material, which is available to authorized users.

Early selection of bZIP73 facilitated adaptation of japonica rice to cold climates

Cold stress is a major factor limiting production and geographic distribution of rice (Oryza sativa). Although the growth range of japonica subspecies has expanded northward compared to modern wild rice (O. rufipogon), the molecular basis of the adaptation remains unclear. Here we report bZIP73, a bZIP transcription factor-coding gene with only one functional polymorphism (+511 G>A) between the two subspecies japonica and indica, may have facilitated japonica adaptation to cold climates. We show the japonica version of bZIP73 (bZIP73^Jap) interacts with bZIP71 and modulates ABA levels and ROS homeostasis. Evolutionary and population genetic analyses suggest bZIP73 has undergone balancing selection; the bZIP73^Jap allele has firstly selected from standing variations in wild rice and likely facilitated cold climate adaptation during initial japonica domestication, while the indica allele bZIP73^Ind was subsequently selected for reasons that remain unclear. Our findings reveal early selection of bZIP73^Jap may have facilitated climate adaptation of primitive rice germplasms.

Japonica rice can grow further north than wild or indica rice and is more tolerant of cold climates. Here, the authors show that bZIP73 likely underwent selection in the early phase of rice domestication to facilitate cold tolerance in japonica by modulating ABA and ROS homeostasis.

Overexpression of a wheat (Triticum aestivum L.) bZIP transcription factor gene, TabZIP6, decreased the freezing tolerance of transgenic Arabidopsis seedlings by down-regulating the expression of CBFs

The basic leucine zipper (bZIP) proteins play important roles against abiotic stress in plants, including cold stress. However, most bZIPs involved in plant freezing tolerance are positive regulators. Only a few bZIPs function negatively in cold stress response. In this study, TabZIP6, a Group C bZIP transcription factor gene from common wheat (Triticum aestivum L.), was cloned and characterized. The transcript of TabZIP6 was strongly induced by cold treatment (4 °C). TabZIP6 is a nuclear-localized protein with transcriptional activation activity. Arabidopsis plants overexpressing TabZIP6 showed decreased tolerance to freezing stress. Microarray as well as quantitative real-time PCR (qRT-PCR) analysis showed that CBFs and some key COR genes, including COR47 and COR15B, were down-regulated by cold treatment in TabZIP6-overexpressing Arabidopsis lines. TabZIP6 was capable of binding to the G-box motif and the CBF1 and CBF3 promoters in yeast cells. A yeast two-hybrid assay revealed that TabZIP6, as well as the other two Group S bZIP proteins involved in cold stress tolerance in wheat, Wlip19 and TaOBF1, can form homodimers by themselves and heterodimers with each other. These results suggest that TabZIP6 may function negatively in the cold stress response by binding to the promoters of CBFs, and thereby decreasing the expression of downstream COR genes in TabZIP6-overexpressing Arabidopsis seedlings.

The membrane tethered transcription factor EcbZIP17 from finger millet promotes plant growth and enhances tolerance to abiotic stresses

The occurrence of various stresses, as the outcome of global climate change, results in the yield losses of crop plants. Prospecting of genes in stress tolerant plant species may help to protect and improve their agronomic performance. Finger millet (Eleusine coracana L.) is a valuable source of superior genes and alleles for stress tolerance. In this study, we isolated a novel endoplasmic reticulum (ER) membrane tethered bZIP transcription factor from finger millet, EcbZIP17. Transgenic tobacco plants overexpressing this gene showed better vegetative growth and seed yield compared with wild type (WT) plants under optimal growth conditions and confirmed upregulation of brassinosteroid signalling genes. Under various abiotic stresses, such as 250 mM NaCl, 10% PEG6000, 400 mM mannitol, water withdrawal, and heat stress, the transgenic plants showed higher germination rate, biomass, primary and secondary root formation, and recovery rate, compared with WT plants. The transgenic plants exposed to an ER stress inducer resulted in greater leaf diameter and plant height as well as higher expression of the ER stress-responsive genes BiP, PDIL, and CRT1. Overall, our results indicated that EcbZIP17 improves plant growth at optimal conditions through brassinosteroid signalling and provide tolerance to various environmental stresses via ER signalling pathways.

Genome-wide identification and analysis of the basic leucine zipper (bZIP) transcription factor gene family in Ustilaginoidea virens

The basic leucine zipper (bZIP) transcription factor (TF) family is one of the largest and most diverse TF families widely distributed across the eukaryotes. The bZIP TF family plays an important role in growth, development, and response to abiotic or biotic stresses, which have been well characterized in plants, but not in plant pathogenic fungi. In this study, we performed genome-wide and systematic bioinformatics analysis of bZIP genes in the fungus Ustilaginoidea virens, the causal agent of rice false smut disease. We identified 28 bZIP family members in the U. virens genome by searching for the bZIP domain in predicted genes. The gene structures, motifs, and phylogenetic relationships were analyzed for bZIP genes in U. virens (UvbZIP). Together with bZIP proteins from two other fungi, the bZIP genes can be divided into eight groups according to their phylogenetic relationships. Based on RNA-Seq data, the expression profiles of UvbZIP genes at different infection stages were evaluated. Results showed that 17 UvbZIP genes were up-regulated during the infection period. Furthermore, 11 infection-related UvbZIP genes were investigated under H2O2 stress and the expression level of eight genes were changed, which confirmed their role in stress tolerance and pathogenicity. In summary, our genome-wide systematic characterization and expression analysis of UvbZIP genes provided insight into the molecular function of these genes in U. virens and provides a reference for other pathogens.

Genome-Wide Identification of bZIP Family Genes Involved in Drought and Heat Stresses in Strawberry (Fragaria vesca)

Basic leucine zipper (bZIP) genes are known to play a crucial role in response to various processes in plant as well as abiotic or biotic stress challenges. We have performed an identification and characterization of 50 bZIP genes across the woodland strawberry (Fragaria vesca) genome, which were divided into 10 clades according to the phylogenetic relationship of the strawberry bZIP proteins with those in Arabidopsis and rice. Five categories of intron patterns were observed within basic and hinge regions of the bZIP domains. Some additional conserved motifs have been found with the group specificity. Further, we predicted DNA-binding specificity of the basic and hinge regions as well as dimerization properties of leucine zipper regions, which was consistent with our phylogenetic clade and classified into 20 subfamilies. Across the different developmental stages of 15 organs and two types of fruits, the clade A bZIP members showed different tissue-specific expression patterns and the duplicated genes were differentially regulated, indicating a functional diversification coupled with the expansion of this gene family in strawberry. Under normal growth conditions, mrna11837 and mrna30280 of clade A showed very weak expression levels in organs and fruits, respectively; but higher expression was observed with different set of genes following drought and heat treatment, which may be caused by the separate response pathway between drought and heat treatments.

PhOBF1, a petunia ocs element binding factor, plays an important role in antiviral RNA silencing

Virus-induced gene silencing (VIGS) is a common reverse genetics strategy for characterizing the function of genes in plants. The detailed mechanism governing RNA silencing efficiency triggered by viruses is largely unclear. Here, we reveal that a petunia (Petunia hybrida) ocs element binding factor, PhOBF1, one of the basic leucine zipper (bZIP) transcription factors, was up-regulated by Tobacco rattle virus (TRV) infection. Simultaneous silencing of PhOBF1 and a reporter gene, phytoene desaturase (PDS) or chalcone synthase (CHS), by TRV-based VIGS led to a failure of the development of leaf photobleaching or the white-corollas phenotype. PhOBF1 silencing caused down-regulation of RNA silencing-related genes, including RNA-dependent RNA polymerases (RDRs), Dicer-like RNase III enzymes (DCLs), and Argonautes (AGOs). After inoculation with the TRV-PhPDS, PhOBF1-RNAi lines exhibited a substantially impaired PDS silencing efficiency, whereas overexpression of PhOBF1 resulted in a recovery of the silencing phenotype (photobleaching) in systemic leaves. A compromised resistance to TRV and Tobacco mosaic virus was found in PhOBF1-RNAi lines, while PhOBF1-overexpressing lines displayed an enhanced resistance to their infections. Compared with wild-type plants, PhOBF1-silenced plants accumulated lower levels of free salicylic acid (SA), salicylic acid glucoside, and phenylalanine, contrarily to higher levels of those in plants overexpressing PhOBF1. Furthermore, transcripts of a number of genes associated with the shikimate and phenylpropanoid pathways were decreased or increased in PhOBF1-RNAi or PhOBF1-overexpressing lines, respectively. Taken together, the data suggest that PhOBF1 regulates TRV-induced RNA silencing efficiency through modulation of RDRs, DCLs, and AGOs mediated by the SA biosynthesis pathway.

Expression of a grape (Vitis vinifera) bZIP transcription factor, VlbZIP36, in Arabidopsis thaliana confers tolerance of drought stress during seed germination and seedling establishment

Drought is one of the most serious factors that limit agricultural productivity and there is considerable interest in understanding the molecular bases of drought responses and their regulation. While numbers of basic leucine zipper (bZIP) transcription factors (TFs) are known to play key roles in response of plants to various abiotic stresses, only a few group K bZIP TFs have been functionally characterized in the context of stress signaling. In this study, we characterized the expression of the grape (Vitis vinifera) group K bZIP gene, VlbZIP36, and found evidence for its involvement in response to drought and the stress-associated phytohormone abscisic acid (ABA). Transgenic Arabidopsis thaliana lines over-expressing VlbZIP36 under the control of a constitutive promoter showed enhanced dehydration tolerance during the seed germination stage, as well as in the seedling and mature plant stages. The results indicated that VlbZIP36 plays a role in drought tolerance by improving the water status, through limiting water loss, and mitigating cellular damage. The latter was evidenced by reduced cell death, lower electrolyte leakage in the transgenic plants, as well as by increased activities of antioxidant enzymes. We concluded that VlbZIP36 enhances drought tolerance through the transcriptional regulation of ABA-/stress-related genes.

The phylogeny of C/S1 bZIP transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of S1 transcripts

Basic leucine zippers (bZIPs) form a large plant transcription factor family. C and S1 bZIP groups can heterodimerize, fulfilling crucial roles in seed development and stress response. S1 sequences also harbor a unique regulatory mechanism, termed Sucrose-Induced Repression of Translation (SIRT). The conservation of both C/S1 bZIP interactions and SIRT remains poorly characterized in non-model species, leaving their evolutionary origin uncertain and limiting crop research. In this work, we explored recently published plant sequencing data to establish a detailed phylogeny of C and S1 bZIPs, investigating their intertwined role in plant evolution, and the origin of SIRT. Our analyses clarified C and S1 bZIP orthology relationships in angiosperms, and identified S1 sequences in gymnosperms. We experimentally showed that the gymnosperm orthologs are regulated by SIRT, tracing back the origin of this unique regulatory mechanism to the ancestor of seed plants. Additionally, we discovered an earlier S ortholog in the charophyte algae Klebsormidium flaccidum, together with a C ortholog. This suggests that C and S groups originated by duplication from a single algal proto-C/S ancestor. Based on our observations, we propose a model wherein the C/S1 bZIP dimer network evolved in seed plants from pre-existing C/S bZIP interactions.

Analysis of basic leucine zipper genes and their expression during bud dormancy in peach (Prunus persica)

Dormancy is a biological characteristic developed to resist the cold conditions in winter. The bZIP transcription factors are present exclusively in eukaryotes and have been identified and classified in many species. bZIP proteins are known to regulate numerous biological processes, however, the role of bZIP in bud dodormancy has not been studied extensively. In total, 50 PpbZIP transcription factor-encoding genes were identified and categorized them into 10 groups (A-I and S). Similar intron/exon structures, additional conserved motifs, and DNA-binding site specificity supported our classification scheme. Additionally, chromosomal distribution and collinearity analyses suggested that expansion of the PpbZIP transcription factor family was due to segment/chromosomal duplications. We also predicted the dimerization properties based on characteristic features of the leucine zipper and classified PpbZIP proteins into 23 subfamilies. Furthermore, qRT-PCR results indicated that PpbZIPs genes may be involved in regulating dormancy. The same gene of different species might participate in different regulating networks through interactions with specific partners. Our expression profiling results complemented the microarray data, suggesting that co-expression patterns of bZIP transcription factors during dormancy differed among deciduous fruit trees. Our findings further clarify the molecular characteristics of the PpbZIP transcription factor family, including potential gene functions during dormancy. This information may facilitate further research on the evolutionary history and biological functions of bZIP proteins in peach and other rosaceae plants.

OeFAD8, OeLIP and OeOSM expression and activity in cold-acclimation of Olea europaea, a perennial dicot without winter-dormancy

Cold-acclimation genes in woody dicots without winter-dormancy, e.g., olive-tree, need investigation. Positive relationships between OeFAD8, OeOSM , and OeLIP19 and olive-tree cold-acclimation exist, and couple with increased lipid unsaturation and cutinisation. Olive-tree is a woody species with no winter-dormancy and low frost-tolerance. However, cold-tolerant genotypes were empirically selected, highlighting that cold-acclimation might be acquired. Proteins needed for olive-tree cold-acclimation are unknown, even if roles for osmotin (OeOSM) as leaf cryoprotectant, and seed lipid-transfer protein for endosperm cutinisation under cold, were demonstrated. In other species, FAD8, coding a desaturase producing α-linolenic acid, is activated by temperature-lowering, concomitantly with bZIP-LIP19 genes. The research was focussed on finding OeLIP19 gene(s) in olive-tree genome, and analyze it/their expression, and that of OeFAD8 and OeOSM, in drupes and leaves under different cold-conditions/developmental stages/genotypes, in comparison with changes in unsaturated lipids and cell wall cutinisation. Cold-induced cytosolic calcium transients always occurred in leaves/drupes of some genotypes, e.g., Moraiolo, but ceased in others, e.g., Canino, at specific drupe stages/cold-treatments, suggesting cold-acclimation acquisition only in the latter genotypes. Canino and Moraiolo were selected for further analyses. Cold-acclimation in Canino was confirmed by an electrolyte leakage from leaf/drupe membranes highly reduced in comparison with Moraiolo. Strong increases in fruit-epicarp/leaf-epidermis cutinisation characterized cold-acclimated Canino, and positively coupled with OeOSM expression, and immunolocalization of the coded protein. OeFAD8 expression increased with cold-acclimation, as the production of α-linolenic acid, and related compounds. An OeLIP19 gene was isolated. Its levels changed with a trend similar to OeFAD8. All together, results sustain a positive relationship between OeFAD8, OeOSM and OeLIP19 expression in olive-tree cold-acclimation. The parallel changes in unsaturated lipids and cutinisation concur to suggest orchestrated roles of the coded proteins in the process.

A Cold-Inducible DEAD-Box RNA Helicase from Arabidopsis thaliana Regulates Plant Growth and Development under Low Temperature

DEAD-box RNA helicases comprise a large family and are involved in a range of RNA processing events. Here, we identified one of the Arabidopsis thaliana DEAD-box RNA helicases, AtRH7, as an interactor of Arabidopsis COLD SHOCK DOMAIN PROTEIN 3 (AtCSP3), which is an RNA chaperone involved in cold adaptation. Promoter:GUS transgenic plants revealed that AtRH7 is expressed ubiquitously and that its levels of the expression are higher in rapidly growing tissues. Knockout mutant lines displayed several morphological alterations such as disturbed vein pattern, pointed first true leaves, and short roots, which resemble ribosome-related mutants of Arabidopsis. In addition, aberrant floral development was also observed in rh7 mutants. When the mutants were germinated at low temperature (12°C), both radicle and first leaf emergence were severely delayed; after exposure of seedlings to a long period of cold, the mutants developed aberrant, fewer, and smaller leaves. RNA blots and circular RT-PCR revealed that 35S and 18S rRNA precursors accumulated to higher levels in the mutants than in WT under both normal and cold conditions, suggesting the mutants are partially impaired in pre-rRNA processing. Taken together, the results suggest that AtRH7 affects rRNA biogenesis and plays an important role in plant growth under cold.

Enhanced Gene Expression Rather than Natural Polymorphism in Coding Sequence of the OsbZIP23 Determines Drought Tolerance and Yield Improvement in Rice Genotypes

Drought is one of the major limiting factors for productivity of crops including rice (Oryza sativa L.). Understanding the role of allelic variations of key regulatory genes involved in stress-tolerance is essential for developing an effective strategy to combat drought. The bZIP transcription factors play a crucial role in abiotic-stress adaptation in plants via abscisic acid (ABA) signaling pathway. The present study aimed to search for allelic polymorphism in the OsbZIP23 gene across selected drought-tolerant and drought-sensitive rice genotypes, and to characterize the new allele through overexpression (OE) and gene-silencing (RNAi). Analyses of the coding DNA sequence (CDS) of the cloned OsbZIP23 gene revealed single nucleotide polymorphism at four places and a 15-nucleotide deletion at one place. The single-copy OsbZIP23 gene is expressed at relatively higher level in leaf tissues of drought-tolerant genotypes, and its abundance is more in reproductive stage. Cloning and sequence analyses of the OsbZIP23-promoter from drought-tolerant O. rufipogon and drought-sensitive IR20 cultivar showed variation in the number of stress-responsive cis-elements and a 35-nucleotide deletion at 5’-UTR in IR20. Analysis of the GFP reporter gene function revealed that the promoter activity of O. rufipogon is comparatively higher than that of IR20. The overexpression of any of the two polymorphic forms (1083 bp and 1068 bp CDS) of OsbZIP23 improved drought tolerance and yield-related traits significantly by retaining higher content of cellular water, soluble sugar and proline; and exhibited decrease in membrane lipid peroxidation in comparison to RNAi lines and non-transgenic plants. The OE lines showed higher expression of target genes-OsRab16B, OsRab21 and OsLEA3-1 and increased ABA sensitivity; indicating that OsbZIP23 is a positive transcriptional-regulator of the ABA-signaling pathway. Taken together, the present study concludes that the enhanced gene expression rather than natural polymorphism in coding sequence of OsbZIP23 is accountable for improved drought tolerance and yield performance in rice genotypes.

Transcriptome Analysis of Salt Stress Responsiveness in the Seedlings of Dongxiang Wild Rice (Oryza rufipogon Griff.)

Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.), and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. The analysis results for the sequencing data showed that 6,867 transcripts were differentially expressed in the leaves (2,216 up-regulated and 4,651 down-regulated) and 4,988 transcripts in the roots (3,105 up-regulated and 1,883 down-regulated). Among these differentially expressed genes, the detection of many transcription factor genes demonstrated that multiple regulatory pathways were involved in salt stress tolerance. In addition, the differentially expressed genes were compared with the previous RNA-Seq analysis of salt-stress responses in cultivated rice Nipponbare, indicating the possible specific molecular mechanisms of salt-stress responses for Dongxiang wild rice. A large number of the salt-inducible genes identified in this study were co-localized onto fine-mapped salt-tolerance-related quantitative trait loci, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for salt-stress tolerance in rice.

Evolutionary and Expression Analyses of the Apple Basic Leucine Zipper Transcription Factor Family

Transcription factors (TFs) play essential roles in the regulatory networks controlling many developmental processes in plants. Members of the basic leucine (Leu) zipper (bZIP) TF family, which is unique to eukaryotes, are involved in regulating diverse processes, including flower and vascular development, seed maturation, stress signaling, and defense responses to pathogens. The bZIP proteins have a characteristic bZIP domain composed of a DNA-binding basic region and a Leu zipper dimerization region. In this study, we identified 112 apple (Malus domestica Borkh) bZIP TF-encoding genes, termed MdbZIP genes. Synteny analysis indicated that segmental and tandem duplication events, as well as whole genome duplication, have contributed to the expansion of the apple bZIP family. The family could be divided into 11 groups based on structural features of the encoded proteins, as well as on the phylogenetic relationship of the apple bZIP proteins to those of the model plant Arabidopsis thaliana (AtbZIP genes). Synteny analysis revealed that several paired MdbZIP genes and AtbZIP gene homologs were located in syntenic genomic regions. Furthermore, expression analyses of group A MdbZIP genes showed distinct expression levels in 10 different organs. Moreover, changes in these expression profiles in response to abiotic stress conditions and various hormone treatments identified MdbZIP genes that were responsive to high salinity and drought, as well as to different phytohormones.

Divergence of the bZIP Gene Family in Strawberry, Peach, and Apple Suggests Multiple Modes of Gene Evolution after Duplication

The basic leucine zipper (bZIP) transcription factors are the most diverse members of dimerizing transcription factors. In the present study, 50, 116, and 47 bZIP genes were identified in Malus domestica (apple), Prunus persica (peach), and Fragaria vesca (strawberry), respectively. Species-specific duplication was the main contributor to the large number of bZIPs observed in apple. After WGD in apple genome, orthologous bZIP genes corresponding to strawberry on duplicated regions in apple genome were retained. However, in peach ancestor, these syntenic regions were quickly lost or deleted. Maybe the positive selection contributed to the expansion of clade S to adapt to the development and environment stresses. In addition, purifying selection was mainly responsible for bZIP sequence-specific DNA binding. The analysis of orthologous pairs between chromosomes indicates that these orthologs derived from one gene duplication located on one of the nine ancient chromosomes in the Rosaceae. The comparative analysis of bZIP genes in three species provides information on the evolutionary fate of bZIP genes in apple and peach after they diverged from strawberry.

Basic leucine zipper (bZIP) transcription factors involved in abiotic stresses: A molecular model of a wheat bZIP factor and implications of its structure in function

BACKGROUND

Basic leucine zipper (bZIP) genes encode transcription factors (TFs) that control important biochemical and physiological processes in plants and all other eukaryotic organisms.

SCOPE OF REVIEW

Here we present (i) the homo-dimeric structural model of bZIP consisting of basic leucine zipper and DNA binding regions, in complex with the synthetic Abscisic Acid-Responsive Element (ABREsyn); (ii) discuss homo- and hetero-dimerisation patterns of bZIP TFs; (iii) summarise the current progress in understanding the molecular mechanisms of function of bZIP TFs, including features determining the specificity of their binding to DNA cis-elements, and (iv) review information on interaction partners of bZIPs during plant development and stress response, as well as on types and roles of post-translational modifications, and regulatory aspects of protein-degradation mediated turn-over. Finally, we (v) recapitulate on the recent advances regarding functional roles of bZIP factors in major agricultural crops, and discuss the potential significance of bZIP-based genetic engineering in improving crop yield and tolerance to abiotic stresses.

MAJOR CONCLUSIONS

An accurate analysis and understanding of roles of plant bZIP TFs in different biological processes requires the knowledge of interacting partners, time and location of expression in plant organs, and the information on mechanisms of homo- and hetero-dimerisation of bZIP TFs.

GENERAL SIGNIFICANCE

Studies on molecular mechanisms of plant bZIP TFs at the atomic levels will provide novel insights into the regulatory processes during plant development, and responses to abiotic and biotic stresses.

A novel wheat bZIP transcription factor, TabZIP60, confers multiple abiotic stress tolerances in transgenic Arabidopsis

The basic region/leucine zipper (bZIP) transcription factors (TFs) play vital roles in the response to abiotic stress. However, little is known about the function of bZIP genes in wheat abiotic stress. In this study, we report the isolation and functional characterization of the TabZIP60 gene. Three homologous genome sequences of TabZIP60 were isolated from hexaploid wheat and mapped to the wheat homoeologous group 6. A subcellular localization analysis indicated that TabZIP60 is a nuclear-localized protein that activates transcription. Furthermore, TabZIP60 gene transcripts were strongly induced by polyethylene glycol, salt, cold and exogenous abscisic acid (ABA) treatments. Further analysis showed that the overexpression of TabZIP60 in Arabidopsis resulted in significantly improved tolerances to drought, salt, freezing stresses and increased plant sensitivity to ABA in seedling growth. Meanwhile, the TabZIP60 was capable of binding ABA-responsive cis-elements that are present in promoters of many known ABA-responsive genes. A subsequent analysis showed that the overexpression of TabZIP60 led to enhanced expression levels of some stress-responsive genes and changes in several physiological parameters. Taken together, these results suggest that TabZIP60 enhances multiple abiotic stresses through the ABA signaling pathway and that modifications of its expression may improve multiple stress tolerances in crop plants.

The regulatory network of ThbZIP1 in response to abscisic acid treatment

Previously, a bZIP transcription factor from Tamarix hispida, ThbZIP1, was characterized: plants overexpressing ThbZIP1 displayed improved salt stress tolerance but were sensitive to abscisic acid (ABA). In the current study, we further characterized the regulatory network of ThbZIP1 and the mechanism of ABA sensitivity mediated by ThbZIP1. An ABF transcription factor from T. hispida, ThABF1, directly regulates the expression of ThbZIP1. Microarray analysis identified 1662 and 1609 genes that were respectively significantly upregulated or downregulated by ThbZIP1 when exposed to ABA. Gene ontology (GO) analysis showed that the processes including "response to stimulus," "catalytic activity," "binding function," and "metabolic process" were highly altered in ThbZIP1 expressing plants exposed to ABA. The gene expression in ThbZIP1 transformed plants were compared between exposed to ABA and salt on the genome scale. Genes differentially regulated by both salt and ABA treatment only accounted for 9.75% of total differentially regulated genes. GO analysis showed that structural molecule activity, organelle part, membrane-enclosed lumen, reproduction, and reproductive process are enhanced by ABA but inhibited by salt stress. Conversely, immune system and multi-organism process were improved by salt but inhibited by ABA. Transcription regulator activity, enzyme regulator activity, and developmental process were significantly altered by ABA but were not affected by salt stress. Our study provides insights into how ThbZIP1 mediates ABA and salt stress response at the molecular level.

System-wide characterization of bZIP transcription factor proteins involved in infection-related morphogenesis of Magnaporthe oryzae

The basic leucine zipper (bZIP) domain-containing transcription factors (TFs) function as key regulators of cellular growth and differentiation in eukaryotic organisms including fungi. We have previously identified MoAp1 and MoAtf1 as bZIP TFs in Magnaporthe oryzae and demonstrated that they regulate the oxidative stress response and are critical in conidiogenesis and pathogenicity. Studies of bZIP proteins could provide a novel strategy for controlling rice blast, but a systematic examination of the bZIP proteins has not been carried out. Here, we identified 19 additional bZIP TFs and characterized their functions. We found that the majority of these TFs exhibit active functions, most notably, in conidiogenesis. We showed that MoHac1 regulates the endoplasmic reticulum stress response through a conserved unfolded protein response pathway, MoMetR controls amino acid metabolism to govern growth and differentiation, and MoBzip10 governs appressorium function and invasive hyphal growth. Moreover, MoBzip5 participates in appressorium formation through a pathway distinct from that MoBzip10, and MoMeaB appears to exert a regulatory role through nutrient uptake and nitrogen utilization. Collectively, our results provide insights into shared and specific functions associated with each of these TFs and link the regulatory roles to the fungal growth, conidiation, appressorium formation, host penetration and pathogenicity.