HY5 is involved in strigolactone-dependent seed germination in Arabidopsis

A soybean bZIP transcription factor is involved in submergence resistance

Although the functions of basic leucine zipper (bZIP) family transcription factors in the regulation of various abiotic stresses are beginning to be unveiled, the precise roles of bZIP proteins in plants coping with submergence stress remain unclear. Here we identified a bZIP gene GmbZIP71-4 from soybean, which localized in the nucleus. The GmbZIP71-4 over-expressed tabocco line showed reduced submergence resistance due to the decreased abscisic acid (ABA) content. GO and KEGG pathway analysis based on chromatin immunoprecipitation assay sequencing (ChIP-seq) indicated that the differences expressed genes between submergence treatment and control groups were specially enriched in plant hormone signal transduction items, especially those in response to ABA. Electrophoretic mobility shift assays (EMSA) demonstrated that GmbZIP71-4 bound to the promoter of GmABF2 gene, which is consistent with the ChIP-qPCR results. GmbZIP71-4 function as a negative regulator of soybean in responding to submergence stress through manipulating ABA signaling pathway. This findings will set a solid foundation for the understanding of submergence resistance in plants.

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.

PfbZIP85 Transcription Factor Mediates ω-3 Fatty Acid-Enriched Oil Biosynthesis by Down-Regulating PfLPAT1B Gene Expression in Plant Tissues

The basic leucine zipper (bZIP) transcription factor (TF) family is one of the biggest TF families identified so far in the plant kingdom, functioning in diverse biological processes including plant growth and development, signal transduction, and stress responses. For Perilla frutescens, a novel oilseed crop abundant in polyunsaturated fatty acids (PUFAs) (especially α-linolenic acid, ALA), the identification and biological functions of bZIP members remain limited. In this study, 101 PfbZIPs were identified in the perilla genome and classified into eleven distinct groups (Groups A, B, C, D, E, F, G, H, I, S, and UC) based on their phylogenetic relationships and gene structures. These PfbZIP genes were distributed unevenly across 18 chromosomes, with 83 pairs of them being segmental duplication genes. Moreover, 78 and 148 pairs of orthologous bZIP genes were detected between perilla and Arabidopsis or sesame, respectively. PfbZIP members belonging to the same subgroup exhibited highly conserved gene structures and functional domains, although significant differences were detected between groups. RNA-seq and RT-qPCR analysis revealed differential expressions of 101 PfbZIP genes during perilla seed development, with several PfbZIPs exhibiting significant correlations with the key oil-related genes. Y1H and GUS activity assays evidenced that PfbZIP85 downregulated the expression of the PfLPAT1B gene by physical interaction with the promoter. PfLPAT1B encodes a lysophosphatidate acyltransferase (LPAT), one of the key enzymes for triacylglycerol (TAG) assembly. Heterogeneous expression of PfbZIP85 significantly reduced the levels of TAG and UFAs (mainly C18:1 and C18:2) but enhanced C18:3 accumulation in both seeds and non-seed tissues in the transgenic tobacco lines. Furthermore, these transgenic tobacco plants showed no significantly adverse phenotype for other agronomic traits such as plant growth, thousand seed weight, and seed germination rate. Collectively, these findings offer valuable perspectives for understanding the functions of PfbZIPs in perilla, particularly in lipid metabolism, showing PfbZIP85 as a suitable target in plant genetic improvement for high-value vegetable oil production.

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.

Analysis of bZIP gene family in lotus (Nelumbo) and functional study of NnbZIP36 in regulating anthocyanin synthesis

BACKGROUND

The basic leucine zipper (bZIP) family is a predominant group of transcription factors in plants, involved in regulating plant growth, development, and response to stressors. Additionally, the bZIP gene family has a key role in anthocyanin production. Despite the significant role of bZIP genes in plants, their potential contribution in lotus remains understudied.

RESULTS

A total of 124 bZIP genes (59 NnbZIPs and 65 NlbZIPs) were identified from genomes of two lotus species. These genes were classified into 13 groups according to the grouping principle of the Arabidopsis bZIP gene family. Analysis of promoter cis-acting elements indicated that most bZIP gene family members in lotus are associated with response to abiotic stresses. The promoters of some bZIP genes contain MYB binding sites that regulate anthocyanin synthesis. We examined the anthocyanin content of the petals from three different colored lotus, combined with transcriptome data analysis and qRT-PCR results, showing that the expression trends of NnbZIP36 and the homologous gene NlbZIP38 were significantly correlated with the anthocyanin content in lotus petals. Furthermore, we found that overexpression of NnbZIP36 in Arabidopsis promoted anthocyanin accumulation by upregulating the expression of genes (4CL, CHI, CHS, F3H, F3'H, DFR, ANS and UF3GT) related to anthocyanin synthesis.

CONCLUSIONS

Our study enhances the understanding of the bZIP gene family in lotus and provides evidence for the role of NnbZIP36 in regulating anthocyanin synthesis. This study also sets the stage for future investigations into the mechanism by which the bZIP gene family regulates anthocyanin biosynthesis in lotus.

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

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

Genomic characterization of bZIP transcription factors related to andrographolide biosynthesis in Andrographis paniculata

The basic leucine zipper (bZIP) transcription factor family plays an important role in various biological processes in plants. Andrographis paniculata (Burm.f) Nees, belonging to the family Acanthaceae, has been widely used as an important traditional herb with a wide range of pharmacological activities, such as antivenom, antiretroviral, anticancer and so on. However, there was no comprehensive analysis of bZIP gene family in the Andrographis paniculata been reported. In this study, we identified 62 bZIPs in Andrographis paniculata and grouped them into 12 subfamilies through the phylogenetic tree analysis. The bZIPs in the same groups have similar motif composition, exon-intron structure and domain distribution. In addition, the RNA-seq data gave a reference for selecting candidate bZIPs to make further function verification. Lastly, qRT-PCR analyses revealed seven ApbZIPs (ApbZIP4, ApbZIP19, ApbZIP30, ApbZIP42, ApbZIP50, ApbZIP52, ApbZIP62) were the most highly expressed in leaf and significantly up-regulated with MeJA and ABA treatment which may be involved in biosynthesis regulation of andrographolide. These data pave the way for further revealing the function of the bZIPs in Andrographis paniculata.

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

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

Genome-wide identification and characterization of bZIP gene family and cloning of candidate genes for anthocyanin biosynthesis in pomegranate (Punica granatum)

BACKGROUND

The basic leucine zipper (bZIP) transcription factor is one of the most abundant and conserved gene families in eukaryotes. In addition to participating in plant development and growth, bZIP transcription factors play crucial roles in various abiotic stress responses and anthocyanin accumulation. Up to now, analysis of bZIP gene family members in pomegranate (Punica granatum) has not been reported. Three published pomegranate genome sequences provide valuable resources for further gene function analysis.

RESULTS

Using bioinformatics analysis, 65 PgbZIPs were identified and analyzed from the 'Taishanhong' pomegranate genome. We divided them into 13 groups (A, B, C, D, E, F, G, H, I, J, K, M, and S) according to the phylogenetic relationship with those of Arabidopsis, each containing a different number of genes. The regularity of exon/intron number and distribution was consistent with the classification of groups in the evolutionary tree. Transcriptome analysis of different tissues showed that members of the PgbZIP gene family were differentially expressed in different developmental stages and tissues of pomegranate. Among them, we selected PgbZIP16 and PgbZIP34 as candidate genes which affect anthocyanin accumulation. The full-length CDS region of PgbZIP16 and PgbZIP34 were cloned from pomegranate petals by homologous cloning technique, encoding 170 and 174 amino acids, which were 510 bp and 522 bp, respectively. Subcellular localization assays suggested that both PgbZIP16 and PgbZIP34 were nucleus-localized. Real-time quantitative PCR (qPCR) was used to explore the expression of PgbZIP16 and PgbZIP34 in the petals of three kinds of ornamental pomegranates at the full flowering stage. The results demonstrated that the expression of PgbZIP16 in red petals was 5.83 times of that in white petals, while PgbZIP34 was 3.9 times. The results of transient expression in tobacco showed that consistent trends were observed in anthocyanin concentration and expression levels of related genes, which both increased and then decreased. Both PgbZIP16 and PgbZIP34 could promote anthocyanin accumulation in tobacco leaves. We obtained transgenic strains overexpressing PgbZIP16, and the histochemical staining for GUS activity showed that overexpressed PgbZIP16 seedlings were expressed in the stem. Transgenic experiments indicated that overexpression of PgbZIP16 significantly upregulated UF3GT, ANS and DFR genes in Arabidopsis and enhanced anthocyanin accumulation.

CONCLUSIONS

The whole genome identification, gene structure, phylogeny, gene cloning, subcellular location and functional verification of the pomegranate bZIP gene family provide a theoretical foundation for the functional study of the PgbZIP gene family and candidate genes for anthocyanin biosynthesis.

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

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

GR24, A Synthetic Strigolactone Analog, and Light Affect the Organization of Cortical Microtubules in Arabidopsis Hypocotyl Cells

Strigolactones are plant hormones regulating cytoskeleton-mediated developmental events in roots, such as lateral root formation and elongation of root hairs and hypocotyls. The latter process was addressed herein by the exogenous application of a synthetic strigolactone, GR24, and an inhibitor of strigolactone biosynthesis, TIS108, on hypocotyls of wild-type Arabidopsis and a strigolactone signaling mutant max2-1 (more axillary growth 2-1). Owing to the interdependence between light and strigolactone signaling, the present work was extended to seedlings grown under a standard light/dark regime, or under continuous darkness. Given the essential role of the cortical microtubules in cell elongation, their organization and dynamics were characterized under the conditions of altered strigolactone signaling using fluorescence microscopy methods with different spatiotemporal capacities, such as confocal laser scanning microscopy (CLSM) and structured illumination microscopy (SIM). It was found that GR24-dependent inhibition of hypocotyl elongation correlated with changes in cortical microtubule organization and dynamics, observed in living wild-type and max2-1 seedlings stably expressing genetically encoded fluorescent molecular markers for microtubules. Quantitative assessment of microscopic datasets revealed that chemical and/or genetic manipulation of strigolactone signaling affected microtubule remodeling, especially under light conditions. The application of GR24 in dark conditions partially alleviated cytoskeletal rearrangement, suggesting a new mechanistic connection between cytoskeletal behavior and the light-dependence of strigolactone signaling.

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.

Genome-Wide Analysis, Characterization, and Expression Profile of the Basic Leucine Zipper Transcription Factor Family in Pineapple

This study identified 57 basic leucine zipper (bZIP) genes from the pineapple genome, and the analysis of these bZIP genes was focused on the evolution and divergence after multiple duplication events in relation to the pineapple genome fusion. According to bioinformatics analysis of a phylogenetic tree, the bZIP gene family was divided into 11 subgroups in pineapple, Arabidopsis, and rice; gene structure and conserved motif analyses showed that bZIP genes within the same subgroup shared similar intron-exon organizations and motif composition. Further synteny analysis showed 17 segmental duplication events with 27 bZIP genes. The study also analyzed the pineapple gene expression of bZIP genes in different tissues, organs, and developmental stages, as well as in abiotic stress responses. The RNA-sequencing data showed that AcobZIP57 was upregulated in all tissues, including vegetative and reproductive tissues. AcobZIP28 and AcobZIP43 together with the other 25 bZIP genes did not show high expression levels in any tissue. Six bZIP genes were exposed to abiotic stress, and the relative expression levels were detected by quantitative real-time PCR. A significant response was observed for AcobZIP24 against all kinds of abiotic stresses at 24 and 48 h in pineapple root tissues. Our study provides a perspective for the evolutionary history and general biological involvement of the bZIP gene family of pineapple, which laid the foundation for future functional characterization of the bZIP genes in pineapple.

Arabidopsis FHY3 and FAR1 integrate light and strigolactone signaling to regulate branching

Branching/tillering is an important parameter of plant architecture and is tightly regulated by both internal factors (such as plant hormones) and external factors (such as light conditions). How the various signaling pathways converge to coordinately regulate branching is not well understood. Here, we report that in Arabidopsis, FHY3 and FAR1, two homologous transcription factors essential for phytochrome A-mediated light signaling, and SMXL6/SMXL7/SMXL8, three key repressors of the strigolactone (SL) signaling pathway, directly interact with SPL9 and SPL15 and suppress their transcriptional activation of BRC1, a key repressor of branching, thus promoting branching. In addition, FHY3 and FAR1 also directly up-regulate the expression of SMXL6 and SMXL7 to promote branching. Simulated shade treatment reduces the accumulation of FHY3 protein, leading to increased expression of BRC1 and reduced branching. Our results establish an integrated model of light and SL coordinately regulating BRC1 expression and branching through converging at the BRC1 promoter.

In plants, branching is regulated by both hormones and external cues such as light. Here the authors show that in Arabidopsis, the phytochrome A-signaling components FHY3 and FAR1, and SMXL proteins that repress strigolactone signaling, both interact with SPL proteins to control expression of the branching regulator BRC1.

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 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.

Strigolactones, karrikins and beyond

The plant hormones strigolactones are synthesized from carotenoids and signal via the α/β hydrolase DWARF 14 (D14) and the F-box protein MORE AXILLARY GROWTH 2 (MAX2). Karrikins, molecules produced upon fire, share MAX2 for signalling, but depend on the D14 paralog KARRIKIN INSENSITIVE 2 (KAI2) for perception with strong evidence that the MAX2-KAI2 protein complex might also recognize so far unknown plant-made karrikin-like molecules. Thus, the phenotypes of the max2 mutants are the complex consequence of a loss of both D14-dependent and KAI2-dependent signalling, hence, the reason why some biological roles, attributed to strigolactones based on max2 phenotypes, could never be observed in d14 or in the strigolactone-deficient max3 and max4 mutants. Moreover, the broadly used synthetic strigolactone analog rac-GR24 has been shown to mimic strigolactone as well as karrikin(-like) signals, providing an extra level of complexity in the distinction of the unique and common roles of both molecules in plant biology. Here, a critical overview is provided of the diverse biological processes regulated by strigolactones and/or karrikins. These two growth regulators are considered beyond their boundaries, and the importance of the yet unknown karrikin-like molecules is discussed as well.

Transcriptional mechanisms associated with seed dormancy and dormancy loss in the gibberellin-insensitive sly1-2 mutant of Arabidopsis thaliana

While widespread transcriptome changes were previously observed with seed dormancy loss, this study specifically characterized transcriptional changes associated with the increased seed dormancy and dormancy loss of the gibberellin (GA) hormone-insensitive sleepy1-2 (sly1-2) mutant. The SLY1 gene encodes the F-box subunit of an SCF E3 ubiquitin ligase needed for GA-triggered proteolysis of DELLA repressors of seed germination. DELLA overaccumulation in sly1-2 seeds leads to increased dormancy that can be rescued without DELLA protein destruction either by overexpression of the GA receptor, GA-INSENSITIVE DWARF1b (GID1b-OE) (74% germination) or by extended dry after-ripening (11 months, 51% germination). After-ripening of sly1 resulted in different transcriptional changes in early versus late Phase II of germination that were consistent with the processes known to occur. Approximately half of the transcriptome changes with after-ripening appear to depend on SLY1-triggered DELLA proteolysis. Given that many of these SLY1/GA-dependent changes are genes involved in protein translation, it appears that GA signaling increases germination capacity in part by activating translation. While sly1-2 after-ripening was associated with transcript-level changes in 4594 genes over two imbibition timepoints, rescue of sly1-2 germination by GID1b-OE was associated with changes in only 23 genes. Thus, a big change in sly1-2 germination phenotype can occur with relatively little change in the global pattern of gene expression during the process of germination. Most GID1b-OE-responsive transcripts showed similar changes with after-ripening in early Phase II of imbibition, but opposite changes with after-ripening by late Phase II. This suggests that GID1b-OE stimulates germination early in imbibition, but may later trigger negative feedback regulation.

The Multifaceted Roles of HY5 in Plant Growth and Development

ELONGATED HYPOCOTYL5 (HY5), a member of the bZIP transcription factor family, inhibits hypocotyl growth and lateral root development, and promotes pigment accumulation in a light-dependent manner in Arabidopsis. Recent research on its role in different processes such as hormone, nutrient, abiotic stress (abscisic acid, salt, cold), and reactive oxygen species signaling pathways clearly places HY5 at the center of a transcriptional network hub. HY5 regulates the transcription of a large number of genes by directly binding to cis-regulatory elements. Recently, HY5 has also been shown to activate its own expression under both visible and UV-B light. Moreover, HY5 acts as a signal that moves from shoot to root to promote nitrate uptake and root growth. Here, we review recent advances on HY5 research in diverse aspects of plant development and highlight still open questions that need to be addressed in the near future for a complete understanding of its function in plant signaling and beyond.

Strigolactone biology: genes, functional genomics, epigenetics and applications

Strigolactones (SLs) represent an important new plant hormone class marked by their multifunctional role in plant and rhizosphere interactions. These compounds stimulate hyphal branching in arbuscular mycorrhizal fungi (AMF) and seed germination of root parasitic plants. In addition, they are involved in the control of plant architecture by inhibiting bud outgrowth as well as many other morphological and developmental processes together with other plant hormones such as auxins and cytokinins. The biosynthetic pathway of SLs that are derived from carotenoids was partially decrypted based on the identification of mutants from a variety of plant species. Only a few SL biosynthetic and regulated genes and related regulatory transcription factors have been identified. However, functional genomics and epigenetic studies started to give first elements on the modality of the regulation of SLs related genes. Since they control plant architecture and plant-rhizosphere interaction, SLs start to be used for agronomical and biotechnological applications. Furthermore, the genes involved in the SL biosynthetic pathway and genes regulated by SL constitute interesting targets for plant breeding. Therefore, it is necessary to decipher and better understand the genetic determinants of their regulation at different levels.

The regulatory network of ThbZIP1 in response to abscisic acid treatment

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

The HY5-PIF regulatory module coordinates light and temperature control of photosynthetic gene transcription

The ability to interpret daily and seasonal alterations in light and temperature signals is essential for plant survival. This is particularly important during seedling establishment when the phytochrome photoreceptors activate photosynthetic pigment production for photoautotrophic growth. Phytochromes accomplish this partly through the suppression of PHYTOCHROME INTERACTING FACTORS (PIFs), negative regulators of chlorophyll and carotenoid biosynthesis. While the bZIP transcription factor LONG HYPOCOTYL 5 (HY5), a potent PIF antagonist, promotes photosynthetic pigment accumulation in response to light. Here we demonstrate that by directly targeting a common promoter cis-element (G-box), HY5 and PIFs form a dynamic activation-suppression transcriptional module responsive to light and temperature cues. This antagonistic regulatory module provides a simple, direct mechanism through which environmental change can redirect transcriptional control of genes required for photosynthesis and photoprotection. In the regulation of photopigment biosynthesis genes, HY5 and PIFs do not operate alone, but with the circadian clock. However, sudden changes in light or temperature conditions can trigger changes in HY5 and PIFs abundance that adjust the expression of common target genes to optimise photosynthetic performance and growth.

Plants, as sessile and photosynthetic organisms, have to constantly adjust their growth and development in response to the environment. While light and temperature are recognized as the most prominent environmental factors modulating plant photosynthetic metabolism, how the seasonal and daily adjustments are achieved is not understood. Global climate alterations will bring together the combination of light and temperature changes and will require an understanding of signal convergence. If we are to mitigate the impact of variable weather patterns on agriculture, it is critical to advance our understanding of the basis of plant responses to environmental variations. In our study we show that the antagonistic activity of key plant transcription factors involved in phytochrome red light photoreceptors signaling (PIFs and HY5) optimize photosynthetic pigment production in response to environmental cues. These light and temperature responsive transcription factors operate in cooperation with the circadian clock to regulate photosynthetic pigment production through a common gene promoter element.

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.

Light as stress factor to plant roots - case of root halotropism

Despite growing underground, largely in darkness, roots emerge to be very sensitive to light. Recently, several important papers have been published which reveal that plant roots not only express all known light receptors but also that their growth, physiology and adaptive stress responses are light-sensitive. In Arabidopsis, illumination of roots speeds-up root growth via reactive oxygen species-mediated and F-actin dependent process. On the other hand, keeping Arabidopsis roots in darkness alters F-actin distribution, polar localization of PIN proteins as well as polar transport of auxin. Several signaling components activated by phytohormones are overlapping with light-related signaling cascade. We demonstrated that the sensitivity of roots to salinity is altered in the light-grown Arabidopsis roots. Particularly, light-exposed roots are less effective in their salt-avoidance behavior known as root halotropism. Here we discuss these new aspects of light-mediated root behavior from cellular, physiological and evolutionary perspectives.