RF2a, a bZIP transcriptional activator of the phloem-specific rice tungro bacilliform virus promoter, functions in vascular development

In silico analysis identified bZIP transcription factors genes responsive to abiotic stress in Alfalfa (Medicago sativa L.)

BACKGROUND

Alfalfa (Medicago sativa L.) is the most cultivated forage legume around the world. Under a variety of growing conditions, forage yield in alfalfa is stymied by biotic and abiotic stresses including heat, salt, drought, and disease. Given the sessile nature of plants, they use strategies including, but not limited to, differential gene expression to respond to environmental cues. Transcription factors control the expression of genes that contribute to or enable tolerance and survival during periods of stress. Basic-leucine zipper (bZIP) transcription factors have been demonstrated to play a critical role in regulating plant growth and development as well as mediate the responses to abiotic stress in several species, including Arabidopsis thaliana, Oryza sativa, Lotus japonicus and Medicago truncatula. However, there is little information about bZIP transcription factors in cultivated alfalfa.

RESULT

In the present study, 237 bZIP genes were identified in alfalfa from publicly available sequencing data. Multiple sequence alignments showed the presence of intact bZIP motifs in the identified sequences. Based on previous phylogenetic analyses in A. thaliana, alfalfa bZIPs were similarly divided and fell into 10 groups. The physico-chemical properties, motif analysis and phylogenetic study of the alfalfa bZIPs revealed high specificity within groups. The differential expression of alfalfa bZIPs in a suite of tissues indicates that bZIP genes are specifically expressed at different developmental stages in alfalfa. Similarly, expression analysis in response to ABA, cold, drought and salt stresses, indicates that a subset of bZIP genes are also differentially expressed and likely play a role in abiotic stress signaling and/or tolerance. RT-qPCR analysis on selected genes further verified these differential expression patterns.

CONCLUSIONS

Taken together, this work provides a framework for the future study of bZIPs in alfalfa and presents candidate bZIPs involved in stress-response signaling.

Mechanically induced localisation of SECONDARY WALL INTERACTING bZIP is associated with thigmomorphogenic and secondary cell wall gene expression

Plant growth requires the integration of internal and external cues, perceived and transduced into a developmental programme of cell division, elongation and wall thickening. Mechanical forces contribute to this regulation, and thigmomorphogenesis typically includes reducing stem height, increasing stem diameter, and a canonical transcriptomic response. We present data on a bZIP transcription factor involved in this process in grasses. Brachypodium distachyon SECONDARY WALL INTERACTING bZIP (SWIZ) protein translocated into the nucleus following mechanostimulation. Classical touch-responsive genes were upregulated in B. distachyon roots following touch, including significant induction of the glycoside hydrolase 17 family, which may be unique to grass thigmomorphogenesis. SWIZ protein binding to an E-box variant in exons and introns was associated with immediate activation followed by repression of gene expression. SWIZ overexpression resulted in plants with reduced stem and root elongation. These data further define plant touch-responsive transcriptomics and physiology, offering insights into grass mechanotranduction dynamics.

The melon Fom-1-Prv resistance gene pair: Correlated spatial expression and interaction with a viral protein

The head-to-head oriented pair of melon resistance genes, Fom-1 and Prv, control resistance to Fusarium oxysporum races 0 and 2 and papaya ringspot virus (PRSV), respectively. They encode, via several RNA splice variants, TIR-NBS-LRR proteins, and Prv has a C-terminal extra domain with a second NBS homologous sequence. In other systems, paired R-proteins were shown to operate by "labor division," with one protein having an extra integrated domain that directly binds the pathogen's Avr factor, and the second protein executing the defense response. We report that the expression of the two genes in two pairs of near-isogenic lines was higher in the resistant isoline and inducible by F. oxysporum race 2 but not by PRSV. The intergenic DNA region separating the coding sequences of the two genes acted as a bi-directional promoter and drove GUS expression in transgenic melon roots and transgenic tobacco plants. Expression of both genes was strong in melon root tips, around the root vascular cylinder, and the phloem and xylem parenchyma of tobacco stems and petioles. The pattern of GUS expression suggests coordinated expression of the two genes. In agreement with the above model, Prv's extra domain was shown to interact with the cylindrical inclusion protein of PRSV both in yeast cells and in planta.

Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild Watermelon

Drought stress has detrimental effects on crop productivity worldwide. A strong root system is crucial for maintaining water and nutrients uptake under drought stress. Wild watermelons possess resilient roots with excellent drought adaptability. However, the genetic factors controlling this trait remain uninvestigated. In this study, we conducted a bulk segregant analysis (BSA) on an F2 population consisting of two watermelon genotypes, wild and domesticated, which differ in their lateral root development under drought conditions. We identified two quantitative trait loci (qNLR_Dr. Chr01 and qNLR_Dr. Chr02) associated with the lateral root response to drought. Furthermore, we determined that a small region (0.93 Mb in qNLR_Dr. Chr01) is closely linked to drought adaptation through quantitative trait loci (QTL) validation and fine mapping. Transcriptome analysis of the parent roots under drought stress revealed unique effects on numerous genes in the sensitive genotype but not in the tolerant genotype. By integrating BSA, fine mapping, and the transcriptome, we identified six genes, namely L-Ascorbate Oxidase (AO), Cellulose Synthase-Interactive Protein 1 (CSI1), Late Embryogenesis Abundant Protein (LEA), Zinc-Finger Homeodomain Protein 2 (ZHD2), Pericycle Factor Type-A 5 (PFA5), and bZIP transcription factor 53-like (bZIP53-like), that might be involved in the drought adaptation. Our findings provide valuable QTLs and genes for marker-assisted selection in improving water-use efficiency and drought tolerance in watermelon. They also lay the groundwork for the genetic manipulation of drought-adapting genes in watermelon and other Cucurbitacea species.

Molecular insights into the responses of barley to yellow mosaic disease through transcriptome analysis

BACKGROUND

Barley (Hordeum vulgare L.) represents the fourth most essential cereal crop in the world, vulnerable to barley yellow mosaic virus (BaYMV) and/or barley mild mosaic virus (BaMMV), leading to the significant yield reduction. To gain a better understanding of the mechanisms regarding barley crop tolerance to virus infection, we employed a transcriptome sequencing approach and investigated global gene expression among three barley varieties under both infected and control conditions.

RESULTS

High-throughput sequencing outputs revealed massive genetic responses, reflected by the barley transcriptome after BaYMV and/or BaMMV infection. Significant enrichments in peptidase complex and protein processing in endoplasmic reticulum were clustered through Gene ontology and KEGG analysis. Many genes were identified as transcription factors, antioxidants, disease resistance genes and plant hormones and differentially expressed between infected and uninfected barley varieties. Importantly, general response genes, variety-specific and infection-specific genes were also discovered. Our results provide useful information for future barley breeding to resist BaYMV and BaMMV.

CONCLUSIONS

Our study elucidates transcriptomic adaptations in barley response to BaYMV/BaMMV infection through high-throughput sequencing technique. The analysis outcome from GO and KEGG pathways suggests that BaYMV disease induced regulations in multiple molecular-biology processes and signalling pathways. Moreover, critical DEGs involved in defence and stress tolerance mechanisms were displayed. Further functional investigations focusing on these DEGs contributes to understanding the molecular mechanisms of plant response to BaYMV disease infection, thereby offering precious genetic resources for breeding barley varieties resistant to BaYMV disease.

The Role of Plant Transcription Factors in the Fight against Plant Viruses

Plants are vulnerable to the challenges of unstable environments and pathogen infections due to their immobility. Among various stress conditions, viral infection is a major threat that causes significant crop loss. In response to viral infection, plants undergo complex molecular and physiological changes, which trigger defense and morphogenic pathways. Transcription factors (TFs), and their interactions with cofactors and cis-regulatory genomic elements, are essential for plant defense mechanisms. The transcriptional regulation by TFs is crucial in establishing plant defense and associated activities during viral infections. Therefore, identifying and characterizing the critical genes involved in the responses of plants against virus stress is essential for the development of transgenic plants that exhibit enhanced tolerance or resistance. This article reviews the current understanding of the transcriptional control of plant defenses, with a special focus on NAC, MYB, WRKY, bZIP, and AP2/ERF TFs. The review provides an update on the latest advances in understanding how plant TFs regulate defense genes expression during viral infection.

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.

Promoter cloning of PuLOX2S gene from "Nanguo" pears and screening of transcription factors by Y1H technique

Our previous study on differential proteome and transcriptome of refrigerated "Nanguo" pears found that the PuLOX2S gene was very active in the LOX pathway of aroma synthesis, but the regulation of expression behavior of the gene and how to mediate the aroma synthesis were still unknown. Partial genome sequences of PuLOX2S were cloned, and its promoter was analyzed by Tail-PCR. The PuLOX2S promoter sequences of 610 bp were isolated and identified using Plant CARE, which were composed of cis-acting elements, such as ABRE, AE-box, ARE, CAAT-box, Box 4, TCCC-motif, CAT-box, CGTCA-motif, G-Box, TATA-box, TCA-element, TGA-element, and TGACG-motif. The Y1H technology was used to determine whether proteins interacted with PuLOX2S based on the pGADT7-Chinese white pear cDNA library. The Y1H results were shown that 52 proteins could interact with the PuLOX2S promoter, which was compared with sequences in the GenBank database. The three genes PuERF12, PuMYB44, and PuRF2a were the candidate transcription factors of PuLOX2S and PuCDPK10 played an important role in the gene expression in Nanguo pears. Therefore, the results of this study supply important information for revealing new function of PuLOX2S and the regulation mechanism of expression behavior of the gene. It provides new ideas for the regulation of aroma synthesis in Nanguo pears. PRACTICAL APPLICATIONS: The gene PuLOX2S was very active in the LOX pathway of aroma synthesis, but the regulation of expression behavior of the gene and how to mediate the aroma synthesis were still unknown. We have successfully cloned the partial sequence of the gene and the 610 bp promoter sequence upstream of PuLOX2S and analyzed the structure of cis-acting elements. There are 52 proteins that interact with the PuLOX2S promoter revealed by the Y1H technique. Three transcription factors among the proteins can regulate the level of PuLOX2S expression, which provides new ideas for the regulation of aroma synthesis in "Nanguo" pears. Moreover, the study results could supply scientific information for the quality improvement and genetic modification of Nanguo pears.

Genome-wide identification and expression analysis of the bZIP transcription factors, and functional analysis in response to drought and cold stresses in pear (Pyrus breschneideri)

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.

Ingeniería genética contra estrés abiótico en cultivos neotropicales: osmolitos, factores de transcripción y CRISPR/Cas9

El neotrópico es sitio de origen de gran variedad de plantas que actualmente son cultivadas con éxito en diferentes regiones del mundo. Sin embargo, condiciones climáticas adversas, que se pueden ver acrecentadas por efectos del cambio climático antropogénico, pueden afectar su rendimiento y productividad debido a las situaciones de estrés abiótico que se pueden generar. Como alternativa para contrarrestar estos efectos, se ha experimentado con modificaciones genéticas, particularmente en genes relacionados con la producción de osmolitos y factores de transcripción que han llevado a que estas plantas, a nivel experimental, tengan mayor tolerancia a estrés oxidativo, altas y bajas temperaturas y fotoinhibición, sequía y salinidad, mediante la acumulación de osmoprotectores, la regulación en la expresión de genes y cambios en el fenotipo. En este trabajo se presentan y describen las estrategias metodológicas planteadas con estos fines y se complementan con ejemplos de trabajos realizados en cultivos de origen neotropical de importancia económica, como maíz, algodón, papa y tomate. Además, y debido a la novedad y potencial que ofrece la edición génica por medio del sistema CRISPR/Cas9, también se mencionan trabajos realizados en plantas con origen neotropical, enfocados en comprender e implementar mecanismos de tolerancia a sequía. Las metodologías aquí descritas podrían constituirse en opciones prácticas para mejorar la seguridad alimentaria con miras a contrarrestar las consecuencias negativas del cambio climático antropogénico.

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.

The vernalization-induced long non-coding RNA VAS functions with the transcription factor TaRF2b to promote TaVRN1 expression for flowering in hexaploid wheat

Vernalization is a physiological process in which prolonged cold exposure establishes flowering competence in winter plants. In hexaploid wheat, TaVRN1 is a cold-induced key regulator that accelerates floral transition. However, the molecular mechanism underlying the gradual activation of TaVRN1 during the vernalization process remains unknown. In this study, we identified the novel transcript VAS (TaVRN1 alternative splicing) as a non-coding RNA derived from the sense strand of the TaVRN1 gene only in winter wheat, which regulates TaVRN1 transcription for flowering. VAS was induced during the early period of vernalization, and its overexpression promoted TaVRN1 expression to accelerate flowering in winter wheat. VAS physically associates with TaRF2b and facilitates docking of the TaRF2b-TaRF2a complex at the TaVRN1 promoter during the middle period of vernalization. TaRF2b recognizes the Sp1 motif within the TaVRN1 proximal promoter region, which is gradually exposed along with the disruption of a loop structure at the TaVRN1 locus during vernalization, to activate the transcription of TaVRN1. The tarf2b mutants exhibited delayed flowering, whereas transgenic wheat lines overexpressing TaRF2b showed earlier flowering. Taken together, our data reveal a distinct regulatory mechanism by which a long non-coding RNA facilitates the transcription factor targeting to regulate wheat flowering, providing novel insights into the vernalization process and a potential target for wheat genetic improvement.

Comparative Transcriptome Analysis of Rice Resistant and Susceptible Genotypes to Xanthomonas oryzae pv. oryzae Identifies Novel Genes to Control Bacterial Leaf Blight

The bacterial leaf blight in rice caused by Xanthomonas oryzae pv. oryzae (Xoo) affects crop losses worldwide. In spite of developing resistant varieties by introgressing different Xa genes, the occurrence of diseases is evident. Here we report identification of several genes that are associated with improved plant immunity against Xoo in a resistant genotype BPT-5204 in comparison with susceptible genotype TN-1. The RNA sequencing information was developed to identify the genes that could provide durable resistance in rice. Xoo-resistant rice genotype BPT-5204 with Xa 5, 13 and 21 genes is compared with sensitive Taichung Native 1 (TN-1) to identify the genetic pathways and gene networks involved in resistance mechanisms. The higher levels of salicylic acid resulted in upregulation of many pathogenesis-related (PR) and redox protein encoding transcripts which resulted in higher hypersensitive response in BPT-5204. Many Serine/threonine protein kinase, leucine-rich repeat (LRR) transmembrane protein kinase, protein kinase family genes, Wall-associated kinase (WAK) were upregulated that resulted in activation of bZIP, WRKY, MYB, DOF and HSFs transcription factors that are associated with improved plant immunity. The study provided roles of many genes and their associated plant immunity pathways that can be used for developing resistant rice cultivars.

Transcription Factor ChbZIP1 from Alkaliphilic Microalgae Chlorella sp. BLD Enhancing Alkaline Tolerance in Transgenic Arabidopsis thaliana

Saline-alkali soil has become an important environmental problem for crop productivity. One of the most effective approaches is to cultivate new stress-tolerant plants through genetic engineering. Through RNA-seq analysis and RT-PCR validation, a novel bZIP transcription factor ChbZIP1, which is significantly upregulated at alkali conditions, was obtained from alkaliphilic microalgae Chlorella sp. BLD. Overexpression of ChbZIP1 in Saccharomyces cerevisiae and Arabidopsis increased their alkali resistance, indicating ChbZIP1 may play important roles in alkali stress response. Through subcellular localization and transcriptional activation activity analyses, we found that ChbZIP1 is a nuclear-localized bZIP TF with transactivation activity to bind with the motif of G-box 2 (TGACGT). Functional analysis found that genes such as GPX1, DOX1, CAT2, and EMB, which contained G-box 2 and were associated with oxidative stress, were significantly upregulated in Arabidopsis with ChbZIP1 overexpression. The antioxidant ability was also enhanced in transgenic Arabidopsis. These results indicate that ChbZIP1 might mediate plant adaptation to alkali stress through the active oxygen detoxification pathway. Thus, ChbZIP1 may contribute to genetically improving plants’ tolerance to alkali stress.

Genome-Wide Identification and Expression Analysis of the Strawberry FvbZIP Gene Family and the Role of Key Gene FabZIP46 in Fruit Resistance to Gray Mold

A total of 54 FvbZIP genes were identified from the strawberry genome. These genes were found to be unevenly distributed on seven different chromosomes, and two of the genes had no matching chromosomal localization. FvbZIP genes were divided into 10 subfamilies according to protein sequence, and the structures of these genes were found to be highly conserved. Based on the bioinformatics analysis of FvbZIP genes, the expression of FabZIP genes changed during different stages of its growth and of its infection with gray mold disease. FabZIP46 was substantially upregulated, and its expression remained relatively high. FabZIP46 was cloned from cultivated strawberries by homologous cloning. The results of a transient transgenic assay revealed that the damage to the fruit tissue was markedly alleviated in strawberries overexpressing FabZIP46, with the incidence rate being substantially lower than that in the control group. By contrast, a brief silencing of FabZIP46 had the opposite effect. The results revealed that FabZIP46 played a positive role in the resistance of strawberries to Botrytis cinerea. The study findings provide valuable insights into the role of bZIP transcription factors as well as a theoretical reference for the regulation of resistance to gray mold disease in strawberry fruit.

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.

Transcriptome analysis of responses in Brachypodium distachyon overexpressing the BdbZIP26 transcription factor

BACKGROUND

Biotic and abiotic stresses are the major cause of reduced growth, persistence, and yield in agriculture. Over the past decade, RNA-Sequencing and the use of transgenics with altered expression of stress related genes have been utilized to gain a better understanding of the molecular mechanisms leading to salt tolerance in a variety of species. Identification of transcription factors that, when overexpressed in plants, improve multiple stress tolerance may be valuable for crop improvement, but sometimes overexpression leads to deleterious effects during normal plant growth.

RESULTS

Brachypodium constitutively expressing the BdbZIP26:GFP gene showed reduced stature compared to wild type plants (WT). RNA-Seq analysis comparing WT and bZIP26 transgenic plants revealed 7772 differentially expressed genes (DEGs). Of these DEGs, 987 of the DEGs were differentially expressed in all three transgenic lines. Many of these DEGs are similar to those often observed in response to abiotic and biotic stress, including signaling proteins such as kinases/phosphatases, calcium/calmodulin related proteins, oxidases/reductases, hormone production and signaling, transcription factors, as well as disease responsive proteins. Interestingly, there were many DEGs associated with protein turnover including ubiquitin-related proteins, F-Box and U-box related proteins, membrane proteins, and ribosomal synthesis proteins. Transgenic and control plants were exposed to salinity stress. Many of the DEGs between the WT and transgenic lines under control conditions were also found to be differentially expressed in WT in response to salinity stress. This suggests that the over-expression of the transcription factor is placing the plant in a state of stress, which may contribute to the plants diminished stature.

CONCLUSION

The constitutive expression of BdbZIP26:GFP had an overall negative effect on plant growth and resulted in stunted plants compared to WT plants under control conditions, and a similar response to WT plants under salt stress conditions. The results of gene expression analysis suggest that the transgenic plants are in a constant state of stress, and that they are trying to allocate resources to survive.

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.

Genome-wide identification, phylogeny, evolutionary expansion and expression analyses of bZIP transcription factor family in tartaty buckwheat

Background

In reported plants, the bZIP family is one of the largest transcription factor families. bZIP genes play roles in the light signal, seed maturation, flower development, cell elongation, seed accumulation protein, abiotic and biological stress and other biological processes. While, no detailed identification and genome-wide analysis of bZIP family genes in Fagopyum talaricum (tartary buckwheat) has previously been published. The recently reported genome sequence of tartary buckwheat provides theoretical basis for us to study and discuss the characteristics and expression of bZIP genes in tartary buckwheat based on the whole genome.

Results

In this study, 96 FtbZIP genes named from FtbZIP1 to FtbZIP96 were identified and divided into 11 subfamilies according to their genetic relationship with 70 bZIPs of A. thaliana. FtbZIP genes are not evenly distributed on the chromosomes, and we found tandem and segmental duplication events of FtbZIP genes on 8 tartary buckwheat chromosomes. According to the results of gene and motif composition, FtbZIP located in the same group contained analogous intron/exon organizations and motif composition. By qRT-PCR, we quantified the expression of FtbZIP members in stem, root, leaf, fruit, and flower and during fruit development. Exogenous ABA treatment increased the weight of tartary buckwheat fruit and changed the expressions of FtbZIP genes in group A.

Conclusions

Through our study, we identified 96 FtbZIP genes in tartary buckwheat and synthetically further analyzed the structure composition, evolution analysis and expression pattern of FtbZIP proteins. The expression pattern indicates that FtbZIP is important in the course of plant growth and development of tartary buckwheat. Through comprehensively analyzing fruit weight and FtbZIP genes expression after ABA treatment and endogenous ABA content of tartary buckwheat fruit, ABA may regulate downstream gene expression by regulating the expression of FtPinG0003523300.01 and FtPinG0003196200.01, thus indirectly affecting the fruit development of tartary buckwheat. This will help us to further study the function of FtbZIP genes in the tartary buckwheat growth and improve the fruit of tartary buckwheat.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5882-z) contains supplementary material, which is available to authorized users.

Overexpression of ZmbZIP22 gene alters endosperm starch content and composition in maize and rice

Starch content and composition are major determinants of yield and quality in maize. In recent years, the major genes for starch metabolism have been cloned in this species. However, the role of transcription factors in regulating the starch metabolism pathway remains unclear. The ZmbZIP22 gene encodes a bZIP transcription factor. In our study, plants overexpressing ZmbZIP22 showed reductions in the size of starch granules, the size and weight of seeds, reduced amylose content, and alterations in the chemical structure of starch granules. Also, overexpression of ZmbZIP22 resulted in increases in the contents of soluble sugars and reducing sugars in transgenic rice and maize. ZmbZIP22 promotes the transcription of starch metabolism genes by binding to their promoters. Screening by yeast one-hybrid assays indicated a possible interaction between ZmbZIP22 and the promoters of eight key starch enzyme genes. Collectively, our results indicated that ZmbZIP22 functions as a negative regulator of starch synthesis, and suggest that this occurs through the regulation of key sugar and starch metabolism genes in maize.

OsbZIP81, A Homologue of Arabidopsis VIP1, May Positively Regulate JA Levels by Directly Targetting the Genes in JA Signaling and Metabolism Pathway in Rice

Rice (Oryza sativa L.) is one of the most important food crops in the world. In plants, jasmonic acid (JA) plays essential roles in response to biotic and abiotic stresses. As one of the largest transcription factors (TFs), basic region/leucine zipper motif (bZIP) TFs play pivotal roles through the whole life of plant growth. However, the relationship between JA and bZIP TFs were rarely reported, especially in rice. In this study, we found two rice homologues of Arabidopsis VIP1 (VirE2-interacting protein 1), OsbZIP81, and OsbZIP84. OsbZIP81 has at least two alternative transcripts, OsbZIP81.1 and OsbZIP81.2. OsbZIP81.1 and OsbZIP84 are typical bZIP TFs, while OsbZIP81.2 is not. OsbZIP81.1 can directly bind OsPIOX and activate its expression. In OsbZIP81.1 overexpression transgenic rice plant, JA (Jasmonic Acid) and SA (Salicylic acid) were up-regulated, while ABA (Abscisic acid) was down-regulated. Moreover, Agrobacterium, Methyl Jasmonic Acid (MeJA), and PEG6000 can largely induce OsbZIP81. Based on ChIP-Seq and Random DNA Binding Selection Assay (RDSA), we identified a novel cis-element OVRE (Oryza VIP1 response element). Combining ChIP-Seq and RNA-Seq, we obtained 1332 targeted genes that were categorized in biotic and abiotic responses, including α-linolenic acid metabolism and fatty acid degradation. Together, these results suggest that OsbZIP81 may positively regulate JA levels by directly targeting the genes in JA signaling and metabolism pathway in rice.

Genome-Wide Identification and Expression Analyses of the bZIP Transcription Factor Genes in moso bamboo (Phyllostachys edulis)

The basic leucine zipper (bZIP) transcription factor (TF) family is one of the largest gene families, and play crucial roles in many processes, including stress responses, hormone effects. The TF family also participates in plant growth and development. However, limited information is available for these genes in moso bamboo (Phyllostachys edulis), one of the most important non-timber forest products in the world. In the present study, 154 putative PhebZIP genes were identified in the moso bamboo genome. The phylogenetic analyses indicate that the PhebZIP gene proteins classify into 9 subfamilies and the gene structures and conserved motifs that analyses identified among all PhebZIP proteins suggested a high group-specificity. Microsynteny and evolutionary patterns analyses of the non-synonymous (Ka) and synonymous (Ks) substitution rates and their ratios indicated that paralogous pairs of PhebZIP genes in moso bamboo underwent a large-scale genome duplication event that occurred 7–15 million years ago (MYA). According to promoter sequence analysis, we further selected 18 genes which contain the higher number of cis-regulatory elements for expression analysis. The result showed that these genes are extensively involved in GA-, ABA- and MeJA-responses, with possibly different mechanisms. The tissue-specific expression profiles of PhebZIP genes in five plant tissues/organs/developmental stages suggested that these genes are involved in moso bamboo organ development, especially seed development. Subcellular localization and transactivation activity analysis showed that PhebZIP47 and PhebZIP126 were localized in the nucleus and PhebZIP47 with no transcriptional activation in yeast. Our research provides a comprehensive understanding of PhebZIP genes and may aid in the selection of appropriate candidate genes for further cloning and functional analysis in moso bamboo growth and development, and improve their resistance to stress during their life.

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.

Calcium signalling regulates the functions of the bZIP protein VIP1 in touch responses in Arabidopsis thaliana

BACKGROUND AND AIMS

VIP1 is a bZIP transcription factor in Arabidopsis thaliana. VIP1 and its close homologues transiently accumulate in the nucleus when cells are exposed to hypo-osmotic and/or mechanical stress. Touch-induced root bending is enhanced in transgenic plants overexpressing a repression domain-fused form of VIP1 (VIP1-SRDXox), suggesting that VIP1, possibly with its close homologues, suppresses touch-induced root bending. The aim of this study was to identify regulators of these functions of VIP1 in mechanical stress responses.

METHODS

Co-immunoprecipitation analysis using VIP1-GFP fusion protein expressed in Arabidopsis plants identified calmodulins as VIP1-GFP interactors. In vitro crosslink analysis was performed using a hexahistidine-tagged calmodulin and glutathione S-transferase-fused forms of VIP1 and its close homologues. Plants expressing GFP-fused forms of VIP1 and its close homologues (bZIP59 and bZIP29) were submerged in hypotonic solutions containing divalent cation chelators, EDTA and EGTA, and a potential calmodulin inhibitor, chlorpromazine, to examine their effects on the nuclear-cytoplasmic shuttling of those proteins. VIP1-SRDXox plants were grown on medium containing 40 mm CaCl2, 40 mm MgCl2 or 80 mm NaCl. MCA1 and MCA2 are mechanosensitive calcium channels, and the hypo-osmotic stress-dependent nuclear-cytoplasmic shuttling of VIP1-GFP in the mca1 mca2 double knockout mutant background was examined.

KEY RESULTS

In vitro crosslink products were detected in the presence of CaCl2, but not in its absence. EDTA, EGTA and chlorpromazine all inhibited both the nuclear import and the nuclear export of VIP1-GFP, bZIP59-GFP and bZIP29-GFP. Either 40 mm CaCl2or 80 mm NaCl enhanced the VIP-SRDX-dependent root bending. The nuclear-cytoplasmic shuttling of VIP1 was observed even in the mca1 mca2 mutant.

CONCLUSIONS

VIP1 and its close homologues can interact with calmodulins. Their nuclear-cytoplasmic shuttling requires neither MCA1 nor MCA2, but does require calcium signalling. Salt stress affects the VIP1-dependent regulation of root bending.

Pivotal role of bZIPs in amylose biosynthesis by genome survey and transcriptome analysis in wheat (Triticum aestivum L.) mutants

Starch makes up 70% of the wheat grain, and is an important source of calories for humans, however, the overconsumption of wheat starch may contribute to nutrition-associated health problems. The challenge is to develop resistant starch including high amylose wheat varieties with health benefits. Adapting advance genomic approaches in EMS-induced mutant lines differing in amylose content, basic leucine zipper (bZIP) regulatory factors that may play role in controlling amylose biosynthesis were identified in wheat. bZIP transcription factors are key regulators of starch biosynthesis genes in rice and maize, but their role in regulating these genes in wheat is poorly understood. A genome-wide survey identified 370 wheat bZIPs, clustered in 11 groups, showing variations in amino acids composition and predicted physicochemical properties. Three approaches namely, whole transcriptome sequencing, qRT-PCR, and correlation analysis in contrasting high and low amylose mutants and their parent line identified 24 candidate bZIP (positive and negative regulators), suggesting bZIPs role in high amylose biosynthesis. bZIPs positive role in high amylose biosynthesis is not known. In silico interactome studies of candidate wheat bZIP homologs in Arabidopsis and rice identified their putative functional role. The identified bZIPs are involved in stress-related pathways, flower and seed development, and starch biosynthesis. An in-depth analysis of molecular mechanism of novel candidate bZIPs may help in raising and improving high amylose wheat varieties.

Normal and Abortive Buds Transcriptomic Profiling of Broccoli ogu Cytoplasmic Male Sterile Line and Its Maintainer

Bud abortion is the main factor affecting hybrid seeds’ yield during broccoli cross breeding when using ogura cytoplasmic male sterile (ogu CMS) lines. However, the genes associated with bud abortion are poorly understood. We applied RNA sequencing to analyze the transcriptomes of normal and abortive buds of broccoli maintainer and ogu CMS lines. Functional analysis showed that among the 54,753 annotated unigenes obtained, 74 and 21 differentially expressed genes in common were upregulated and downregulated in ogu CMS abortive buds compared with ogu CMS normal buds, maintainer normal, and abortive buds, respectively. Nineteen of the common differentially expressed genes were enriched by GO terms associated with glycosyl hydrolases, reactive oxygen species scavenging, inhibitor, and protein degradation. Ethylene-responsive transcription factor 115 and transcriptional factor basic helix-loop-helix 137 were significantly upregulated; transcription factors DUO1 and PosF21/RF2a/BZIP34 were downregulated in ogu CMS abortive buds compared with the other groups. Genes related to polygalacturonase metabolism, glycosyl hydrolases, oxidation reduction process, phenylalanine metabolism, and phenylpropanoid biosynthesis were significantly changed in ogu CMS abortive buds. Our results increase our understanding of bud abortion, provide a valuable resource for further functional characterization of ogu CMS during bud abortion, and will aid in future cross breeding of Brassica crops.

Genome-Wide Identification and Structural Analysis of bZIP Transcription Factor Genes in Brassica napus

The basic region/leucine zipper motif (bZIP) transcription factor family is one of the largest families of transcriptional regulators in plants. bZIP genes have been systematically characterized in some plants, but not in rapeseed (Brassica napus). In this study, we identified 247 BnbZIP genes in the rapeseed genome, which we classified into 10 subfamilies based on phylogenetic analysis of their deduced protein sequences. The BnbZIP genes were grouped into functional clades with Arabidopsis genes with similar putative functions, indicating functional conservation. Genome mapping analysis revealed that the BnbZIPs are distributed unevenly across all 19 chromosomes, and that some of these genes arose through whole-genome duplication and dispersed duplication events. All expression profiles of 247 bZIP genes were extracted from RNA-sequencing data obtained from 17 different B. napus ZS11 tissues with 42 various developmental stages. These genes exhibited different expression patterns in various tissues, revealing that these genes are differentially regulated. Our results provide a valuable foundation for functional dissection of the different BnbZIP homologs in B. napus and its parental lines and for molecular breeding studies of bZIP genes in B. napus.

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.

Transcriptome Profiling of the Phaseolus vulgaris - Colletotrichum lindemuthianum Pathosystem

Bean (Phaseolus vulgaris) anthracnose caused by the hemi-biotrophic pathogen Colletotrichum lindemuthianum is a major factor limiting production worldwide. Although sources of resistance have been identified and characterized, the early molecular events in the host-pathogen interface have not been investigated. In the current study, we conducted a comprehensive transcriptome analysis using Illumina sequencing of two near isogenic lines (NILs) differing for the presence of the Co-1 gene on chromosome Pv01 during a time course following infection with race 73 of C. lindemuthianum. From this, we identified 3,250 significantly differentially expressed genes (DEGs) within and between the NILs over the time course of infection. During the biotrophic phase the majority of DEGs were up regulated in the susceptible NIL, whereas more DEGs were up-regulated in the resistant NIL during the necrotrophic phase. Various defense related genes, such as those encoding PR proteins, peroxidases, lipoxygenases were up regulated in the resistant NIL. Conversely, genes encoding sugar transporters were up-regulated in the susceptible NIL during the later stages of infection. Additionally, numerous transcription factors (TFs) and candidate genes within the vicinity of the Co-1 locus were differentially expressed, suggesting a global reprogramming of gene expression in and around the Co-1 locus. Through this analysis, we reduced the previous number of candidate genes reported at the Co-1 locus from eight to three. These results suggest the dynamic nature of P. vulgaris-C. lindemuthianum interaction at the transcriptomic level and reflect the role of both pathogen and effector triggered immunity on changes in plant gene expression.

Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development

Plant bZIP group I transcription factors have been reported mainly for their role during vascular development and osmosensory responses. Interestingly, bZIP29 has been identified in a cell cycle interactome, indicating additional functions of bZIP29 in plant development. Here, bZIP29 was functionally characterized to study its role during plant development. It is not present in vascular tissue but is specifically expressed in proliferative tissues. Genome-wide mapping of bZIP29 target genes confirmed its role in stress and osmosensory responses, but also identified specific binding to several core cell cycle genes and to genes involved in cell wall organization. bZIP29 protein complex analyses validated interaction with other bZIP group I members and provided insight into regulatory mechanisms acting on bZIP dimers. In agreement with bZIP29 expression in proliferative tissues and with its binding to promoters of cell cycle regulators, dominant-negative repression of bZIP29 altered the cell number in leaves and in the root meristem. A transcriptome analysis on the root meristem, however, indicated that bZIP29 might regulate cell number through control of cell wall organization. Finally, ectopic dominant-negative repression of bZIP29 and redundant factors led to a seedling-lethal phenotype, pointing to essential roles for bZIP group I factors early in plant development.

VIP1 is very important/interesting protein 1 regulating touch responses of Arabidopsis

VIP1 (VIRE2-INTERACTING PROTEIN 1) is a bZIP transcription factor in Arabidopsis thaliana. VIP1 and its close homologs (i.e., Arabidopsis group I bZIP proteins) are present in the cytoplasm under steady conditions, but are transiently localized to the nucleus when cells are exposed to hypo-osmotic conditions, which mimic mechanical stimuli such as touch. Recently we have reported that overexpression of a repression domain-fused form of VIP1 represses the expression of some touch-responsive genes, changes structures and/or local auxin responses of the root cap cells, and enhances the touch-induced root waving. This raises the possibility that VIP1 suppresses touch-induced responses. VIP1 should be useful to further characterize touch responses of plants. Here we discuss 2 seemingly interesting perspectives about VIP1: (1) What factors are involved in regulating the nuclear localization of VIP1?; (2) What can be done to further characterize the physiological functions of VIP1 and other Arabidopsis group I bZIP proteins?

The bZIP Protein VIP1 Is Involved in Touch Responses in Arabidopsis Roots

VIP1 is a bZIP transcription factor in Arabidopsis (Arabidopsis thaliana). VIP1 transiently accumulates in the nucleus when cells are exposed to hypoosmotic conditions, but its physiological relevance is unclear. This is possibly because Arabidopsis has approximately 10 close homologs of VIP1 and they function redundantly. To examine their physiological roles, transgenic plants overexpressing a repression domain-fused form of VIP1 (VIP1-SRDXox plants), in which the gene activation mediated by VIP1 is expected to be repressed, were generated. Because hypoosmotic stress can mimic mechanical stimuli (e.g. touch), the touch-induced root-waving phenotypes and gene expression patterns in those transgenic plants were examined. VIP1-SRDXox plants exhibited more severe root waving and lower expression of putative VIP1 target genes. The expression of the VIP1-green fluorescent protein (GFP) fusion protein partially suppressed the VIP1-SRDX-induced increase in root waving when expressed in the VIP1-SRDXox plants. These results suggest that VIP1 can suppress the touch-induced root waving. The VIP1-SRDX-induced increase in root waving was also suppressed when the synthetic auxin 2,4-dichlorophenoxy acetic acid or the ethylene precursor 1-aminocyclopropane-1-carboxylic acid, which is known to activate auxin biosynthesis, was present in the growth medium. Root cap cells with the auxin marker DR5rev::GFP were more abundant in the VIP1-SRDXox background than in the wild-type background. Auxin is transported via the root cap, and the conditions of outermost root cap layers were abnormal in VIP1-SRDXox plants. These results raise the possibility that VIP1 influences structures of the root cap and thereby regulates the local auxin responses in roots.

Monitoring the efficacy of mutated Allium sativum leaf lectin in transgenic rice against Rhizoctonia solani

BACKGROUND

Rice sheath blight, caused by Rhizoctonia solani is one of the most devastating diseases of rice. It is associated with significant reduction in rice productivity worldwide. A mutant variant of mannose binding Allium sativum leaf agglutinin (mASAL) was previously reported to exhibit strong antifungal activity against R. solani. In this study, the mASAL gene has been evaluated for its in planta antifungal activity in rice plants.

RESULTS

mASAL was cloned into pCAMBIA1301 binary vector under the control of CaMV35S promoter. It was expressed in an elite indica rice cv. IR64 by employing Agrobacterium tumefaciens-mediated transformation. Molecular analyses of transgenic plants confirmed the presence and stable integration of mASAL gene. Immunohistofluorescence analysis of various tissue sections of plant parts clearly indicated the constitutive expression of mASAL. The segregation pattern of mASAL transgene was observed in T1 progenies in a 3:1 Mendelian ratio. The expression of mASAL was confirmed in T0 and T1 plants through western blot analysis followed by ELISA. In planta bioassay of transgenic lines against R. solani exhibited an average of 55 % reduction in sheath blight percentage disease index (PDI).

CONCLUSIONS

The present study opens up the possibility of engineering rice plants with the antifungal gene mASAL, conferring resistance to sheath blight.

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.

Isolation and expression analysis of 18 CsbZIP genes implicated in abiotic stress responses in the tea plant (Camellia sinensis)

Basic leucine zipper (bZIP) transcription factors (TFs) play essential roles in regulating stress processes in plants. Despite the economic importance of this woody crop, there is little information about bZIP TFs in tea plants. In this study, 18 bZIP genes were isolated from the tea plant (Camellia sinensis) and named sequentially from CsbZIP1 to CsbZIP18. According to the phylogenetic classification as in Arabidopsis, the CsbZIP genes spanned ten subgroups (Group A, B, C, D, E, F, H, I, S and K) of bZIP TFs. When analyzed for organ specific expression, all CsbZIP genes were found to be ubiquitously expressed in roots, stems, leaves and flowers. Expression analysis of CsbZIP genes in response to four abiotic stresses showed that in leaves, 9, 9, 15 and 11 CsbZIPs have 2-fold greater variation in transcript abundance under cold, exogenous ABA, high salinity and dehydration conditions, respectively. In roots, 5, 12, 14 and 11 CsbZIPs were differentially expressed under conditions of cold, exogenous ABA, high salinity and dehydration stresses. Moreover, CsbZIP genes in Groups F, H, S and K exhibited several folds up-and/or down-regulation against the above four stresses. Notably, CsbZIP18 of group K showed significant up-regulation in response to these same stresses, suggesting a vital functional role in stress response. Together, these findings increase our knowledge of bZIP TFs in the tea plant and suggest the significance of CsbZIP genes in plant abiotic responses.

Synthetic promoters in planta

This paper reviews the importance, prospective and development of synthetic promoters reported in planta. A review of the synthetic promoters developed in planta would help researchers utilize the available resources and design new promoters to benefit fundamental research and agricultural applications. The demand for promoters for the improvement and application of transgenic techniques in research and agricultural production is increasing. Native/naturally occurring promoters have some limitations in terms of their induction conditions, transcription efficiency and size. The strength and specificity of native promoter can be tailored by manipulating its 'cis-architecture' by the use of several recombinant DNA technologies. Newly derived chimeric promoters with specific attributes are emerging as an efficient tool for plant molecular biology. In the last three decades, synthetic promoters have been used to regulate plant gene expression. To better understand synthetic promoters, in this article, we reviewed promoter structure, the scope of cis-engineering, strategies for their development, their importance in plant biology and the total number of such promoters (188) developed in planta to date; we then categorized them under different functional regimes as biotic stress-inducible, abiotic stress-inducible, light-responsive, chemical-inducible, hormone-inducible, constitutive and tissue-specific. Furthermore, we identified a set of 36 synthetic promoters that control multiple types of expression in planta. Additionally, we illustrated the differences between native and synthetic promoters and among different synthetic promoter in each group, especially in terms of efficiency and induction conditions. As a prospective of this review, the use of ideal synthetic promoters is one of the prime requirements for generating transgenic plants suitable for promoting sustainable agriculture and plant molecular farming.

Differential expression of four soybean bZIP genes during Phakopsora pachyrhizi infection

Asian soybean rust (ASR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, is one of most important diseases in the soybean (Glycine max (L.) Merr.) agribusiness. The identification and characterization of genes related to plant defense responses to fungal infection are essential to develop ASR-resistant plants. In this work, we describe four soybean genes, GmbZIP62, GmbZIP105, GmbZIPE1, and GmbZIPE2, which encode transcription factors containing a basic leucine zipper (bZIP) domain from two divergent classes, and that are responsive to P. pachyrhizi infection. Molecular phylogenetic analyses demonstrated that these genes encode proteins similar to bZIP factors responsive to pathogens. Yeast transactivation assays showed that only GmbZIP62 has strong transactivation activity in yeast. In addition, three of the bZIP transcription factors analyzed were also differentially expressed by plant defense hormones, and all were differentially expressed by fungal attack, indicating that these proteins might participate in response to ASR infection. The results suggested that these bZIP proteins are part of the plant defense response to P. pachyrhizi infection, by regulating the gene expression related to ASR infection responses. These bZIP genes are potential targets to obtain new soybean genotypes resistant to ASR.

Differential expression of four soybean bZIP genes during Phakopsora pachyrhizi infection

Asian soybean rust (ASR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, is one of most important diseases in the soybean (Glycine max (L.) Merr.) agribusiness. The identification and characterization of genes related to plant defense responses to fungal infection are essential to develop ASR-resistant plants. In this work, we describe four soybean genes, GmbZIP62, GmbZIP105, GmbZIPE1, and GmbZIPE2, which encode transcription factors containing a basic leucine zipper (bZIP) domain from two divergent classes, and that are responsive to P. pachyrhizi infection. Molecular phylogenetic analyses demonstrated that these genes encode proteins similar to bZIP factors responsive to pathogens. Yeast transactivation assays showed that only GmbZIP62 has strong transactivation activity in yeast. In addition, three of the bZIP transcription factors analyzed were also differentially expressed by plant defense hormones, and all were differentially expressed by fungal attack, indicating that these proteins might participate in response to ASR infection. The results suggested that these bZIP proteins are part of the plant defense response to P. pachyrhizi infection, by regulating the gene expression related to ASR infection responses. These bZIP genes are potential targets to obtain new soybean genotypes resistant to ASR.

Basic leucine zipper family in barley: genome-wide characterization of members and expression analysis

The basic leucine zipper (bZIP) family is one of the largest and most diverse transcription factors in eukaryotes participating in many essential plant processes. We identified 141 bZIP proteins encoded by 89 genes from the Hordeum vulgare genome. HvbZIPs were classified into 11 groups based on their DNA-binding motif. Amino acid sequence alignment of the HvbZIPs basic-hinge regions revealed some highly conserved residues within each group. The leucine zipper heptads were analyzed predicting their dimerization properties. 34 conserved motifs were identified outside the bZIP domain. Phylogenetic analysis indicated that major diversification within the bZIP family predated the monocot/dicot divergence, although intra-species duplication and parallel evolution seems to be occurred afterward. Localization of HvbZIPs on the barley chromosomes revealed that different groups have been distributed on seven chromosomes of barley. Six types of intron pattern were detected within the basic-hinge regions. Most of the detected cis-elements in the promoter and UTR sequences were involved in seed development or abiotic stress response. Microarray data analysis revealed differential expression pattern of HvbZIPs in response to ABA treatment, drought, and cold stresses and during barley grain development and germination. This information would be helpful for functional characterization of bZIP transcription factors in barley.

Basic leucine zipper family in barley: genome-wide characterization of members and expression analysis

The basic leucine zipper (bZIP) family is one of the largest and most diverse transcription factors in eukaryotes participating in many essential plant processes. We identified 141 bZIP proteins encoded by 89 genes from the Hordeum vulgare genome. HvbZIPs were classified into 11 groups based on their DNA-binding motif. Amino acid sequence alignment of the HvbZIPs basic-hinge regions revealed some highly conserved residues within each group. The leucine zipper heptads were analyzed predicting their dimerization properties. 34 conserved motifs were identified outside the bZIP domain. Phylogenetic analysis indicated that major diversification within the bZIP family predated the monocot/dicot divergence, although intra-species duplication and parallel evolution seems to be occurred afterward. Localization of HvbZIPs on the barley chromosomes revealed that different groups have been distributed on seven chromosomes of barley. Six types of intron pattern were detected within the basic-hinge regions. Most of the detected cis-elements in the promoter and UTR sequences were involved in seed development or abiotic stress response. Microarray data analysis revealed differential expression pattern of HvbZIPs in response to ABA treatment, drought, and cold stresses and during barley grain development and germination. This information would be helpful for functional characterization of bZIP transcription factors in barley.

ZmGRF, a GA regulatory factor from maize, promotes flowering and plant growth in Arabidopsis

Transcription factors that act as positive regulators of gibberellin (GA) biosynthetic genes in plants are not well understood. A nuclear-localized basic leucine zipper transcription factor, ZmGRF, was isolated from maize. The core DNA sequence motif recognized for binding by ZmGRF was CCANNTGGC. ZmGRF overexpression in transgenic Arabidopsis plants promoted flowering, stem elongation, and cell expansion. Chromatin immunoprecipitation assays revealed that ZmGRF bound directly to the cis-element CCANNTGGC in the promoter of the Arabidopsis ent-kaurene oxidase (AtKO1) gene and promoted AtKO1 expression. GA4 content increased by 372-567% in transgenic Arabidopsis plants overexpressing ZmGRF compared to wild-type control plants. The GIBBERELLIN-INSENSITIVE DWARF1 gene, which encodes a GA receptor, was also upregulated and the growth-repressing DELLA protein gene GA INSENSITIVE was downregulated. Our results showed ZmGRF functioned through the GA-signaling pathway.

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.

Analysis of functions of VIP1 and its close homologs in osmosensory responses of Arabidopsis thaliana

VIP1 is a bZIP protein in Arabidopsis thaliana. VIP1 accumulates in the nucleus under hypo-osmotic conditions and interacts with the promoters of hypo-osmolarity-responsive genes, CYP707A1 and CYP707A3 (CYP707A1/3), but neither overexpression of VIP1 nor truncation of its DNA-binding region affects the expression of CYP707A3 in vivo, raising the possibility that VIP and other proteins are functionally redundant. Here we show further analyses on VIP1 and its close homologs, namely, Arabidopsis group I bZIP proteins. The patterns of the signals of the GFP-fused group I bZIP proteins were similar in onion and Arabidopsis cells, suggesting that they have similar subcellular localization. In a yeast one-hybrid assay, the group I bZIP proteins caused reporter gene activation in the yeast reporter strain. VIP1 and other group I bZIP proteins showed positive results in a yeast two-hybrid assay and a bimolecular fluorescence complementation assay, suggesting that they physically interact. These results support the idea that they have somewhat similar functions. By gel shift assays, VIP1-binding sequences in the CYP707A1/3 promoters were confirmed to be AGCTGT/G. Their presence in the promoters of the genes that respond to hypo-osmotic conditions was evaluated using previously published microarray data. Interestingly, a significantly higher proportion of the promoters of the genes that were up-regulated by rehydration treatment and/or submergence treatment (treatment by a hypotonic solution) and a significantly lower proportion of the promoters of the genes that were down-regulated by such treatment shared AGCTGT/G. To further assess the physiological role of VIP1, constitutively nuclear-localized variants of VIP1 were generated. When overexpressed in Arabidopsis, some of them as well as VIP1 caused growth retardation under a mannitol-stressed condition, where VIP1 is localized mainly in the cytoplasm. This raises the possibility that the expression of VIP1 itself rather than its nuclear localization is responsible for regulating the mannitol responses.

Genome-wide analysis of the bZIP transcription factors in cucumber

bZIP proteins are one of the largest transcriptional regulators playing crucial roles in plant development, physiological processes, and biotic/abiotic stress responses. Despite the availability of recently published draft genome sequence of Cucumis sativus, no comprehensive investigation of these family members has been presented for cucumber. We have identified 64 bZIP transcription factor-encoding genes in the cucumber genome. Based on structural features of their encoded proteins, CsbZIP genes could be classified into 6 groups. Cucumber bZIP genes were expanded mainly by segmental duplication rather than tandem duplication. Although segmental duplication rate of the CsbZIP genes was lower than that of Arabidopsis, rice and sorghum, it was observed as a common expansion mechanism. Some orthologous relationships and chromosomal rearrangements were observed according to comparative mapping analysis with other species. Genome-wide expression analysis of bZIP genes indicated that 64 CsbZIP genes were differentially expressed in at least one of the ten sampled tissues. A total of 4 CsbZIP genes displayed higher expression values in leaf, flowers and root tissues. The in silico micro-RNA (miRNA) and target transcript analyses identified that a total of 21 CsbZIP genes were targeted by 38 plant miRNAs. CsbZIP20 and CsbZIP22 are the most targeted by miR165 and miR166 family members, respectively. We also analyzed the expression of ten CsbZIP genes in the root and leaf tissues of drought-stressed cucumber using quantitative RT-PCR. All of the selected CsbZIP genes were measured as increased in root tissue at 24th h upon PEG treatment. Contrarily, the down-regulation was observed in leaf tissues of all analyzed CsbZIP genes. CsbZIP12 and CsbZIP44 genes showed gradual induction of expression in root tissues during time points. This genome-wide identification and expression profiling provides new opportunities for cloning and functional analyses, which may be used in further studies for improving stress tolerance in plants.

Genome-wide analysis and expression profile of the bZIP transcription factor gene family in grapevine (Vitis vinifera)

Background

Basic leucine zipper (bZIP) transcription factor gene family is one of the largest and most diverse families in plants. Current studies have shown that the bZIP proteins regulate numerous growth and developmental processes and biotic and abiotic stress responses. Nonetheless, knowledge concerning the specific expression patterns and evolutionary history of plant bZIP family members remains very limited.

Results

We identified 55 bZIP transcription factor-encoding genes in the grapevine (Vitis vinifera) genome, and divided them into 10 groups according to the phylogenetic relationship with those in Arabidopsis. The chromosome distribution and the collinearity analyses suggest that expansion of the grapevine bZIP (VvbZIP) transcription factor family was greatly contributed by the segment/chromosomal duplications, which may be associated with the grapevine genome fusion events. Nine intron/exon structural patterns within the bZIP domain and the additional conserved motifs were identified among all VvbZIP proteins, and showed a high group-specificity. The predicted specificities on DNA-binding domains indicated that some highly conserved amino acid residues exist across each major group in the tree of land plant life. The expression patterns of VvbZIP genes across the grapevine gene expression atlas, based on microarray technology, suggest that VvbZIP genes are involved in grapevine organ development, especially seed development. Expression analysis based on qRT-PCR indicated that VvbZIP genes are extensively involved in drought- and heat-responses, with possibly different mechanisms.

Conclusions

The genome-wide identification, chromosome organization, gene structures, evolutionary and expression analyses of grapevine bZIP genes provide an overall insight of this gene family and their potential involvement in growth, development and stress responses. This will facilitate further research on the bZIP gene family regarding their evolutionary history and biological functions.

Gene SGL, encoding a kinesin-like protein with transactivation activity, is involved in grain length and plant height in rice

Grain shape, a complex agronomic trait, plays an important role in determining yield and quality in rice. In the present study, a mutant named short grain length (sgl) was identified among explants of tissue cultured japonica variety Kita-ake. It exhibited reduced plant height (about 72 % of WT) and short grain length (about 80 % of WT). The reduced length was due to decreased cell elongation. The Short Grain Length (SGL) gene was isolated via map-based cloning and identified to encode a kinesin-like protein. SGL was expressed in the whole plant, especially in the stem and panicles. SGL was shown to have transcriptional activity. In onion epidermal cells, SGL protein was found mainly in the nucleus. Real-time PCR analyses showed that expression levels of genes involved in gibberellin metabolic pathways were affected in the sgl mutant. These data suggested that SGL protein may be involved in regulating GA synthesis and response genes, that in turn, regulates grain length and plant height.

Genomic surveys and expression analysis of bZIP gene family in castor bean (Ricinus communis L.)

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.

The plant-specific dof transcription factors family: new players involved in vascular system development and functioning in Arabidopsis

In higher plants phloem and xylem are responsible for long-distance transport of water, nutrients, and signals that act systemically at short or long-distance to coordinate developmental processes. The formation of the plant vascular system is a complex process that integrates signaling events and gene regulation at transcriptional and posttranscriptional levels. Thanks to transcriptomic and proteomic analysis we start to better understand the mechanisms underlying the formation and the functioning of the vascular system. The role of the DNA-binding with one finger (Dof TFs), a group of plant-specific transcription factors, recently emerged as part of the transcriptional regulatory networks acting on the formation and functioning of the vascular tissues. More than half of the members of this TF family are expressed in the vascular system. In addition some of them have been proposed to be mobile proteins, suggesting a possible role in the control of short- or long-distance signaling as well. This review summarizes the current knowledge on Dof TFs family in Arabidopsis with a special focus on their role in vascular development and functioning.

A bZIP protein, VIP1, is a regulator of osmosensory signaling in Arabidopsis

Abscisic acid is a stress-related phytohormone that has roles in dehydration and rehydration. In Arabidopsis (Arabidopsis thaliana), two genes that inactivate abscisic acid, CYP707A1 and CYP707A3, are rapidly up-regulated upon rehydration. The factors that regulate CYP707A1/3 are not well characterized. We expressed a bZIP protein, VIP1, as a green fluorescent protein fusion protein in Arabidopsis and found that the nuclear localization of VIP1 was enhanced within 10 min after rehydration. A yeast one-hybrid assay revealed that the amino-terminal region of VIP1 has transcriptional activation potential. In a transient reporter assay using Arabidopsis protoplasts, VIP1 enhanced the promoter activities of CYP707A1/3. In gel shift and chromatin immunoprecipitation analyses, VIP1 directly bound to DNA fragments of the CYP707A1/3 promoters. Transgenic plants expressing VIP1-green fluorescent protein were found to overexpress CYP707A1/3 mRNAs. The time course of nuclear-cytoplasmic shuttling of VIP1 was consistent with the time courses of the expression of CYP707A1/3. These results suggest that VIP1 functions as a regulator of osmosensory signaling in Arabidopsis.