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In plants, the bZIP (basic leucine zipper) transcription factors regulate diverse functions, including processes such as plant development and stress response. However, few have been functionally characterized in maize (Zea mays). In this study, we cloned ZmbZIP72, a bZIP transcription factor gene from maize, which had only one copy in the maize genome and harbored three introns. Analysis of the amino acid sequence of Zmb-ZIP72 revealed a highly conserved bZIP DNA-binding domain in its C-terminal region, and four conserved sequences distributed in N- or C-terminal region. The ZmbZIP72 gene expressed differentially in various organs of maize plants and was induced by abscisic acid, high salinity, and drought treatment in seedlings. Subcellular localization analysis in onion epidermal cells indicated that ZmbZIP72 was a nuclear protein. Transactivation assay in yeast demonstrated that ZmbZIP72 functioned as a transcriptional activator and its N terminus (amino acids 23-63) was necessary for the transactivation activity. Heterologous overexpression of ZmbZIP72 improved drought and partial salt tolerance of transgenic Arabidopsis plants, as determined by physiological analyses of leaf water loss, electrolyte leakage, proline content, and survival rate under stress. In addition, the seeds of Zmb-ZIP72-overexpressing transgenic plants were hypersensitive to ABA and osmotic stress. Moreover, overexpression of ZmbZIP72 enhanced the expression of ABA-inducible genes such as RD29B, RAB18, and HIS1-3. These results suggest that the ZmbZIP72 protein functions as an ABA-dependent transcription factor in positive modulation of abiotic stress tolerance and may be a candidate gene with potential application in molecular breeding to enhance stress tolerance in crops.

Background Transcription factors (TFs) are involved in many important biological processes, including cell stretching, histological differentiation, metabolic activity, seed storage, gene regulation, and response to abiotic and biotic stresses. Little is known about the functions, evolutionary history, and expression patterns of basic region-leucine zipper TF family genes in pear, despite the release of the genome of Chinese white pears (“Dangshansuli”). Results Overall, 92 bZIP genes were identified in the pear genome ( Pyrus breschneideri ). Of these, 83 were randomly distributed on all 17 chromosomes except chromosome 4, and the other 9 genes were located on loose scaffolding. The genes were divided into 14 subgroups. Whole-genome duplications, dispersed duplication, and purifying selection for whole-genome duplications are the main reasons for the expansion of the PbrbZIP gene family. The analysis of functional annotation enrichment indicated that most of the functions of PbrbZIP genes were enriched in Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways involved in the abiotic stress response. Next, expression analysis and virus-induced gene silencing results indicated that PbrbZIP genes might play critical roles in response to drought and cold stresses, especially for the genes from subgroups A, C, G, I, and S. Conclusions Ninety-two PbrbZIP genes were identified from the pear genome and classified into 14 subgroups. PbrbZIP genes were mainly expanded from whole-genome duplications and dispersed duplications and retained by purifying selection. PbrbZIP genes were induced by cold and drought stresses and played important roles in drought and cold tolerance. These results provided useful information for further increasing the tolerance of pears to stresses and a foundation to study the cold and drought tolerance mechanism of PbrbZIP genes.

Interaction specificity is a required feature of biological networks and a necessary characteristic of protein or small-molecule reagents and therapeutics. The ability to alter or inhibit protein interactions selectively would advance basic and applied molecular science. Assessing or modelling interaction specificity requires treating multiple competing complexes, which presents computational and experimental challenges. Here we present a computational framework for designing protein-interaction specificity and use it to identify specific peptide partners for human basic-region leucine zipper (bZIP) transcription factors. Protein microarrays were used to characterize designed, synthetic ligands for all but one of 20 bZIP families. The bZIP proteins share strong sequence and structural similarities and thus are challenging targets to bind specifically. Nevertheless, many of the designs, including examples that bind the oncoproteins c-Jun, c-Fos and c-Maf (also called JUN, FOS and MAF, respectively), were selective for their targets over all 19 other families. Collectively, the designs exhibit a wide range of interaction profiles and demonstrate that human bZIPs have only sparsely sampled the possible interaction space accessible to them. Our computational method provides a way to systematically analyse trade-offs between stability and specificity and is suitable for use with many types of structure-scoring functions; thus, it may prove broadly useful as a tool for protein design. Protein family values Designing peptides, proteins or small molecules that bind to native protein targets is a promising route to new reagents and therapies. However, dealing with the interaction specificity problem —that is, achieving designs that are selective for their intended targets in preference to related alternatives — is difficult. Grigoryan et al . have developed a computational framework to design protein–peptide interactions as a step towards avoiding this problem. They used the method to identify peptides that bound to human bZIP transcription factors, and despite the fact that bZIP proteins share strong sequence and structural similarities, the chosen peptides selectively bound to one family, including examples binding to the oncoproteins c-Jun, c-Fos and c-Maf, but not to the 19 other bZIP families. In this manuscript, the authors develop a computational framework to design protein peptide interactions, and they use the method to identify peptides that bind to human bZIP transcription factors. Despite that fact that bZIP proteins share strong sequence and structural similarities, the authors were able to find peptides that selectively bound to one family, but not the 19 other families.

The basic leucine zipper (bZIP) transcription factors comprise a family of transcriptional regulators present extensively in plants, involved in regulating diverse biological processes such as flower and vascular development, seed maturation, stress signaling and pathogen defense. Castor bean (Ricinus communis L. Euphorbiaceae) is one of the most important non-edible oilseed crops and its seed oil is broadly used for industrial applications. We performed a comprehensive genome-wide identification and analysis of the bZIP transcription factors that exist in the castor bean genome in this study. In total, 49 RcbZIP transcription factors were identified, characterized and categorized into 11 groups (I–XI) based on their gene structure, DNA-binding sites, conserved motifs, and phylogenetic relationships. The dimerization properties of 49 RcbZIP proteins were predicted on the basis of the characteristic features in the leucine zipper. Global expression profiles of 49 RcbZIP genes among different tissues were examined using high-throughput sequencing of digital gene expression profiles, and resulted in diverse expression patterns that may provide basic information to further reveal the function of the 49 RcbZIP genes in castor bean. The results obtained from this study would provide valuable information in understanding the molecular basis of the RcbZIP transcription factor family and their potential function in regulating the growth and development, particularly in seed filling of castor bean.

Transcription factors are regulatory proteins known to modulate gene expression. These are the critical component of signaling pathways and help in mitigating various developmental and stress responses. Among them, bZIP, BBR, and BZR transcription factor families are well known to play a crucial role in regulating growth, development, and defense responses. However, limited data is available on these transcription factors in Triticum aestivum . In this study, bZIP, BBR, and BZR sequences from Brachypodium distachyon , Oryza sativa , Oryza barthii , Oryza brachyantha , T . aestivum , Triticum urartu , Sorghum bicolor , Zea mays were retrieved, and dendrograms were constructed to analyze the evolutionary relatedness among them. The sequences clustered into one group indicated a degree of evolutionary correlation highlighting the common lineage of cereal grains. This analysis also exhibited that these genes were highly conserved among studied monocots emphasizing their common ancestry. Furthermore, these transcription factor genes were evaluated for envisaging conserved motifs, gene structure, and subcellular localization in T . aestivum . This comprehensive computational analysis has provided an insight into transcription factor evolution that can also be useful in developing approaches for future functional characterization of these genes in T . aestivum . Furthermore, the data generated can be beneficial in future for genetic manipulation of economically important plants.

Olive (Olea europaea.L) is an economically important oleaginous crop and its fruit cold-pressed oil is used for edible oil all over the world. The basic region-leucine zipper (bZIP) family is one of the largest transcription factors families among eukaryotic organisms; its members play vital roles in environmental signaling, stress response, plant growth, seed maturation, and fruit development. However, a comprehensive report on the bZIP gene family in olive is lacking. In this study, 103 OebZIP genes from the olive genome were identified and divided into 12 subfamilies according to their genetic relationship with 78 bZIPs of A. thaliana. Most OebZIP genes are clustered in the subgroup that has a similar gene structure and conserved motif distribution. According to the characteristics of the leucine zipper region, the dimerization characteristics of 103 OebZIP proteins were predicted. Gene duplication analyses revealed that 22 OebZIP genes were involved in the expansion of the bZIP family. To evaluate the expression patterns of OebZIP genes, RNA-seq data available in public databases were analyzed. The highly expressed OebZIP genes and several lipid synthesis genes (LPGs) in fruits of two varieties with different oil contents during the fast oil accumulation stage were examined via qRT-PCR. By comparing the dynamic changes of oil accumulation, OebZIP1, OebZIP7, OebZIP22, and OebZIP99 were shown to have a close relationship with fruit development and lipid synthesis. Additionally, some OebZIP had a significant positive correlation with various LPG genes. This study gives insights into the structural features, evolutionary patterns, and expression analysis, laying a foundation to further reveal the function of the 103 OebZIP genes in olive.

Key messageThe understanding of roles of bZIP factors in biological processes during plant development and under abiotic stresses requires the detailed mechanistic knowledge of behaviour of TFs.Basic leucine zipper (bZIP) transcription factors (TFs) play key roles in the regulation of grain development and plant responses to abiotic stresses. We investigated the role and molecular mechanisms of function of the TabZIP2 gene isolated from drought-stressed wheat plants. Molecular characterisation of TabZIP2 and derived protein included analyses of gene expression and its target promoter, and the influence of interacting partners on the target promoter activation. Two interacting partners of TabZIP2, the 14-3-3 protein, TaWIN1 and the bZIP transcription factor TaABI5L, were identified in a Y2H screen. We established that under elevated ABA levels the activity of TabZIP2 was negatively regulated by the TaWIN1 protein and positively regulated by the SnRK3/CIPK protein kinase WPK4, reported previously to be responsive to nutrient starvation. The physical interaction between the TaWIN1 and the WPK4 was detected. We also compared the influence of homo- and hetero-dimerisation of TabZIP2 and TaABI5L on DNA binding. TabZIP2 gene functional analyses were performed using drought-inducible overexpression of TabZIP2 in transgenic wheat. Transgenic plants grown under moderate drought during flowering, were smaller than control plants, and had fewer spikes and seeds per plant. However, a single seed weight was increased compared to single seed weights of control plants in three of four evaluated transgenic lines. The observed phenotypes of transgenic plants and the regulation of TabZIP2 activity by nutrient starvation-responsive WPK4, suggest that the TabZIP2 could be the part of a signalling pathway, which controls the rearrangement of carbohydrate and nutrient flows in plant organs in response to drought.

Plant mitochondrial transcription termination factor (mTERF) genes comprise a large family with important roles in regulating organelle gene expression. In this study, a comprehensive database search yielded 31 potential mTERF genes in maize (Zea mays L.) and most of them were targeted to mitochondria or chloroplasts. Maize mTERF were divided into nine main groups based on phylogenetic analysis, and group IX represented the mitochondria and species-specific clade that diverged from other groups. Tandem and segmental duplication both contributed to the expansion of the mTERF gene family in the maize genome. Comprehensive expression analysis of these genes, using microarray data and RNA-seq data, revealed that these genes exhibit a variety of expression patterns. Environmental stimulus experiments revealed differential up or down-regulation expression of maize mTERF genes in seedlings exposed to light/dark, salts and plant hormones, respectively, suggesting various important roles of maize mTERF genes in light acclimation and stress-related responses. These results will be useful for elucidating the roles of mTERF genes in the growth, development and stress response of maize.

Background Drought is one of the major abiotic stresses affecting plant growth, development and crop productivity. ABA responsive element binding factor (ABF) plays an important role in stress responses via regulating the expression of stress-responsive genes. Results In this study, a gene coding for ABF ( PtrABF ) was isolated from Poncirus trifoliata (L.) Raf. PtrABF had a complete open reading frame of 1347 bp, encoding a 448 amino acid peptide, and shared high sequence identities with ABFs from other plants. PtrABF was subcellularly targeted to the nucleus, exhibited transactivation activity in yeast cell and could bind to ABRE, supporting its role as a transcription factor. Expression levels of PtrABF were induced by treatments with dehydration, low temperature and ABA. Ectopic expression of PtrABF under the control of a CaMV 35S promoter in transgenic tobacco plants enhanced tolerance to both dehydration and drought. Under dehydration and drought conditions, the transgenic plants accumulated lower levels of reactive oxygen species compared with wild type, accompanied by higher activities and expression levels of three antioxidant enzymes. In addition, steady-state mRNA levels of nine stress-responsive genes coding for either functional or regulatory proteins were induced to higher levels in the transgenic lines with or without drought stress. Conclusions PtrABF is a bZIP transcription factor and functions in positive modulation of drought stress tolerance. It may be an important candidate gene for molecular breeding of drought- tolerant plants.

Sucrose is known to repress the translation of Arabidopsis thaliana AtbZIP11 transcript which encodes a protein belonging to the group of S (S--stands for small) basic region-leucine zipper (bZIP)-type transcription factor. This repression is called sucrose-induced repression of translation (SIRT). It is mediated through the sucrose-controlled upstream open reading frame (SC-uORF) found in the AtbZIP11 transcript. The SIRT is reported for 4 other genes belonging to the group of S bZIP in Arabidopsis. Tobacco tbz17 is phylogenetically closely related to AtbZIP11 and carries a putative SC-uORF in its 5'-leader region. Here we demonstrate that tbz17 exhibits SIRT mediated by its SC-uORF in a manner similar to genes belonging to the S bZIP group of the Arabidopsis genus. Furthermore, constitutive transgenic expression of tbz17 lacking its 5'-leader region containing the SC-uORF leads to production of tobacco plants with thicker leaves composed of enlarged cells with 3-4 times higher sucrose content compared to wild type plants. Our finding provides a novel strategy to generate plants with high sucrose content.