Genome-wide analysis of the AREB/ABF gene lineage in land plants and functional analysis of TaABF3 in Arabidopsis

Identification and expression of the AREB/ABF/ABI5 subfamily genes in chickpea and lentil reveal major players involved in ABA-mediated defense response to drought stress

MAIN CONCLUSION

This study identified and evaluated the expression of the AREB/ABF/ABI5 subfamily genes in chickpea and lentil, and revealed the major players involved in defense response to PEG-induced drought stress. Abscisic acid (ABA)-responsive element-binding protein/ABRE-binding factor/ABA-INSENSITIVE 5 (AREB/ABF/ABI5) subfamily proteins are major players in the ABA-mediated signaling pathway triggered by multiple stresses. AREB/ABF/ABI5 subfamily proteins belong to the basic-leucine zipper transcription factors that regulate the expression of several downstream defense genes to abiotic and biotic stresses. This protein set is highly targeted when trying to understand plant defense against abiotic stress or to improve plant tolerance to drought, cold, and salinity stresses. However, there is still very little information available about the genes of the AREB/ABF/ABI5 subfamily in chickpea and lentil. Herein, 8 chickpea and 9 lentil genes of the AREB/ABF/ABI5 subfamily were identified based on sequence analysis, and their expression levels were tested in a polyethylene glycol-induced drought experiment (20% PEG in Hoagland solution) using real-time RT-PCR and metadata analysis. Sequence analysis showed that members of this subfamily are highly conserved among themselves and with their orthologous genes in other closely related plant species. Overall, sequence data suggested that these genes may possess close or overlapping biological roles in regulating the transcription of abiotic stress-related defense genes. The meta-analysis from RNA-Seq datasets of unstressed plants showed that some members of this gene subfamily have a tissue-specific expression in both chickpea and lentil. Drought-contrasting chickpea and lentil cultivars showed that most AREB/ABF/ABI5 genes are modulated by PEG-induced drought. Furthermore, AREB/ABF/ABI5 genes had also a tendency for higher expression as cultivar tolerance increases. Therefore, this study identified the AREB/ABF/ABI5 subfamily genes in chickpea and lentil, and provides a comprehensive characterization of these members to support further focused research.

Identification and Functional Validation of the PeDHN Gene Family in Moso Bamboo

As climate change intensifies soil drought and salinization, enhancing the drought and salt tolerance of moso bamboo (Phyllostachys edulis) is urgent. DHN genes are crucial for plant stress responses and have gained attention in plant resistance to drought and salinity. This study identified nine DHN family members (PeDHN1-PeDHN9) from moso bamboo, which were classified into K2S-type, YK2S-type, and Y2K2S-type dehydrins based on their characteristic motifs. We employed integrated bioinformatics approaches to analyze their gene structure, phylogeny, biological properties, and expression patterns under various stress conditions. Five genes (PeDHN2/4/5/6/8), which may have significant functional roles in moso bamboo, were selected for cloning. Subcellular localization experiments showed that YK2S-type dehydrins (PeDHN2/5/6) localized to both the nucleus and the plasma membrane, while K2S-type dehydrins (PeDHN4/8) were exclusively localized to the plasma membrane, indicating functional differentiation. qRT-PCR analysis revealed that the expression of PeDHN2/4/5/6/8 was significantly responsive to stress treatments with ABA, NaCl, and PEG. Additionally, overexpressing these genes in rice significantly enhanced seed germination rates and root development under salt and ABA stress, further confirming that PeDHN2/4/5/6/8 contribute to enhancing plant stress tolerance. Yeast one-hybrid assays demonstrated that two PeABF1 proteins could bind to the promoter of PeDHN4, suggesting that PeDHN4 may regulate stress responses through the ABA signaling pathway. Thus, these findings demonstrate that PeDHN2/4/5/6/8 are closely related to the response of moso bamboo to drought and saline-alkali environments. This research offers insights for moso bamboo cultivation and theoretical foundations for bamboo genetic improvement in stress environments.

Alternative Splicing of BnABF4L Mediates Response to Abiotic Stresses in Rapeseed (Brassica napus L.)

ABRE BINDING FACTOR 4 (ABF4) is a pivotal regulatory gene in the abscisic acid (ABA) signaling pathway, and changes in its expression levels can modulate the plant's stress resistance. To further explore the specific regulatory mechanisms of alternative splicing (AS) in the ABA signaling pathway and to identify new breakthroughs for breeding high stress-resistant varieties of Brassica napus, we identified 17 homologous genes of ABF4 in the genome. Utilizing bioinformatics techniques, we analyzed their motifs, conserved domains, and cis-acting elements of their promoters. Through transcriptome data from the stress-tolerant dwarf strain ndf2 and its parental line 3529, we uncovered a significantly differentially expressed ABF4 gene, which we named BnABF4L. Subsequently, we analyzed the AS events of BnABF4L under normal growth conditions and different abiotic stresses, as well as the impact of different transcript variants' 5' untranslated region (5'UTR) on gene translation. BnABF4L undergoes alternative 3' splice site (A3SS) selection to produce three transcripts (V1-V3) with divergent 5'UTRs. While V1 translation is suppressed by upstream ORFs (uORFs), V2/V3 exhibit enhanced translational efficiency. Under stress, ndf2 shifts splicing toward V3, circumventing uORF-mediated repression to upregulate stress-adapted isoforms. We validated the inhibitory effect of upstream open reading frames (uORFs) on protein-coding open reading frame (pORFs) and, based on the collective experimental results, proposed the flexible regulatory mechanism of AS events of BnABF4L in response to stress. Our findings provide new insights for future studies on stress resistance in rapeseed as well as for research on the regulation of alternative splicing mechanisms in the ABA signaling pathway.

Genome-Wide identification and expression analysis of CsABF/AREB gene family in cucumber (Cucumis sativus L.) and in response to phytohormonal and abiotic stresses

Abscisic acid (ABA)-responsive element binding factors (ABF)/ABA-responsive element binding proteins (AREB)/ABA insensitive protein 5 (ABI5) all belong to the basic leucine zipper (bZIP) transcription factor A subfamily. The bZIP transcription factor family contains 13 subfamilies, namely groups A, B, C, D, E, F, G, H, I, J, K, M and S, and the ABF/AREB/ABI5 gene belongs to A subfamily of the bZIP transcription factor. However, genomic analysis of CsABF/AREB in cucumber (Cucumis sativus L.) has not been systematically studied. In this study, we analyzed the characterization of CsABF/AREB family members and their response to phytohormonal and abiotic stresses. The results showed that a total of 8 genes family members were identified in cucumber. Structural domain analysis showed that the proteins of these family members are highly similar, and all of them belong to the bZIP structural domain. qRT-PCR analysis showed that CsABF/AREB members are expressed in root, stem, and leaf, with the highest expression in root, followed by stem and leaf. In addition, all 8 CsABF/AREB genes respond to ABA and methyl jasmonate (Me-JA). Among them, CsABF7 has the highest expression under both ABA and Me-JA treatments. Drought and salt stress significantly induce CsABF1, CsABF2, CsABF7, and CsABF8 expression. Drought and NaC1 stresses significantly induce the expression of CsABF1, CsABF2, CsABF7, and CsABF8. This study provides a basis for a further understanding of the role of CsABF/AREB homologous genes in response to abiotic stress and lays the foundation for further research on the function of CsABF/AREB.

Horizontally acquired CSP genes contribute to wheat adaptation and improvement

Although horizontal gene transfer (HGT) often facilitates environmental adaptation of recipient organisms, whether and how they might affect crop evolution and domestication is unclear. Here we show that three genes encoding cold-shock proteins (CSPs) were transferred from bacteria to Triticeae, a tribe of the grass family that includes several major staple crops such as wheat, barley and rye. The acquired CSP genes in wheat (TaCSPs) are functionally conserved in their bacterial homologues by encoding a nucleic acid-binding protein. Experimental evidence indicates that TaCSP genes positively regulate drought response and improve photosynthetic efficiency under water-deficient conditions by directly targeting a type 1 metallothionein gene to increase reactive oxygen species scavenging, which in turn contributed to the geographic expansion of wheat. We identified an elite CSP haplotype in Aegilops tauschii, introduction of which to wheat significantly increased drought tolerance, photosynthetic efficiency and grain yields. These findings not only provide major insights into the role of HGT in crop adaptation and domestication, but also demonstrate that novel microbial genes introduced through HGT offer a stable and naturally optimized resource for transgenic crop breeding and improvement.

ZmABF4-ZmVIL2/ZmFIP37 module enhances drought tolerance in maize seedlings

Drought, as a primary environmental factor, imposes significant constraints on developmental processes and productivity of plants. PHDs were identified as stress-responsive genes in a wide range of eukaryotes. However, the regulatory mechanisms governing PHD genes in maize under abiotic stress conditions are still largely unknown and require further investigation. Here, we identified a mutant, zmvil2, in the EMS mutant library with a C to T mutation in the exon of the Zm00001d053875 (VIN3-like protein 2, ZmVIL2), resulting in premature termination of protein coding. ZmVIL2 belongs to PHD protein family. Compared to WT, zmvil2 mutant exhibited increased sensitivity to drought stress. Consistently, overexpression of ZmVIL2 enhances drought resistance in maize. Y2H, BiFC, and Co-IP experiments revealed that ZmVIL2 directly interacts with ZmFIP37 (FKBP12-interacting protein of 37). zmfip37 knockout mutants also exhibit decreased drought tolerance. Interestingly, we demonstrated that ZmABF4 directly binds to the ZmVIL2 promoter to enhance its activity in yeast one hybrid (Y1H), electrophoretic mobility shift assay (EMSA) and dual luciferase reporter assays. Therefore, we uncovered a novel model ZmABF4-ZmVIL2/ZmFIP37 that promotes drought tolerance in maize. Overall, these findings have enriched the knowledge of the functions of PHD genes in maize and provides genetic resources for breeding stress-tolerant maize varieties.

Transcription factor DcbZIPs regulate secondary metabolism in Dendrobium catenatum during cold stress

Cold stress seriously affects plant development and secondary metabolism. The basic region/leucine zipper (bZIP) is one of the largest transcription factor (TFs) family and widely involved in plant cold stress response. However, the function of bZIP in Dendrobium catenatum has not been well-documented. Cold inhibited the growth of D. catenatum and increased total polysaccharide and alkaloid contents in stems. Here, 62 DcbZIP genes were identified in D. catenatum, which were divided into 13 subfamilies. Among them, 58 DcbZIPs responded to cold stress, which were selected based on the transcriptome database produced from cold-treated D. catenatum seedlings. Specifically, the expression of DcbZIP3/6/28 was highly induced by cold treatment in leaves or stems. Gene sequence analysis indicated that DcbZIP3/6/28 contains the bZIP conserved domain and is localized to the cell nucleus. Co-expression networks showed that DcbZIP6 was significantly negatively correlated with PAL2 (palmitoyl-CoA), which is involved in flavonoid metabolism. Moreover, DcbZIP28 has significant negative correlations with various metabolism-related genes in the polysaccharide metabolic pathway, including PFKA1 (6-phosphofructokinase), ALDO2 (aldose-6-phosphate reductase) and SCRK5 (fructokinase). These results implied that DcbZIP6 or DcbZIP28 are mainly involved in flavonoid or polysaccharide metabolism. Overall, these findings provide new insights into the roles of the DcbZIP gene family in secondary metabolism in D. catenatum under cold stress.

BcABF1 Plays a Role in the Feedback Regulation of Abscisic Acid Signaling via the Direct Activation of BcPYL4 Expression in Pakchoi

Abscisic acid-responsive element-binding factor 1 (ABF1), a key transcription factor in the ABA signal transduction process, regulates the expression of downstream ABA-responsive genes and is involved in modulating plant responses to abiotic stress and developmental processes. However, there is currently limited research on the feedback regulation of ABF1 in ABA signaling. This study delves into the function of BcABF1 in Pakchoi. We observed a marked increase in BcABF1 expression in leaves upon ABA induction. The overexpression of BcABF1 not only spurred Arabidopsis growth but also augmented the levels of endogenous IAA. Furthermore, BcABF1 overexpression in Arabidopsis significantly decreased leaf water loss and enhanced the expression of genes associated with drought tolerance in the ABA pathway. Intriguingly, we found that BcABF1 can directly activate BcPYL4 expression, a critical receptor in the ABA pathway. Similar to BcABF1, the overexpression of BcPYL4 in Arabidopsis also reduces leaf water loss and promotes the expression of drought and other ABA-responsive genes. Finally, our findings suggested a novel feedback regulation mechanism within the ABA signaling pathway, wherein BcABF1 positively amplifies the ABA signal by directly binding to and activating the BcPYL4 promoter.

Genome-Wide Identification and Expression Profiling of the ABF Transcription Factor Family in Wheat (Triticum aestivum L.)

Members of the abscisic acid (ABA)-responsive element (ABRE) binding factor (ABF) and ABA-responsive element binding protein (AREB) families play essential roles in the regulation of ABA signaling pathway activity and shape the ability of plants to adapt to a range of stressful environmental conditions. To date, however, systematic genome-wide analyses focused on the ABF/AREB gene family in wheat are lacking. Here, we identified 35 ABF/AREB genes in the wheat genome, designated TaABF1-TaABF35 according to their chromosomal distribution. These genes were further classified, based on their phylogenetic relationships, into three groups (A-C), with the TaABF genes in a given group exhibiting similar motifs and similar numbers of introns/exons. Cis-element analyses of the promoter regions upstream of these TaABFs revealed large numbers of ABREs, with the other predominant elements that were identified differing across these three groups. Patterns of TaABF gene expansion were primarily characterized by allopolyploidization and fragment duplication, with purifying selection having played a significant role in the evolution of this gene family. Further expression profiling indicated that the majority of the TaABF genes from groups A and B were highly expressed in various tissues and upregulated following abiotic stress exposure such as drought, low temperature, low nitrogen, etc., while some of the TaABF genes in group C were specifically expressed in grain tissues. Regulatory network analyses revealed that four of the group A TaABFs (TaABF2, TaABF7, TaABF13, and TaABF19) were centrally located in protein-protein interaction networks, with 13 of these TaABF genes being regulated by 11 known miRNAs, which play important roles in abiotic stress resistance such as drought and salt stress. The two primary upstream transcription factor types found to regulate TaABF gene expression were BBR/BPC and ERF, which have previously been reported to be important in the context of plant abiotic stress responses. Together, these results offer insight into the role that the ABF/AREB genes play in the responses of wheat to abiotic stressors, providing a robust foundation for future functional studies of these genes.

Transcription factors PuPRE6/PuMYB12 and histone deacetylase PuHDAC9-like regulate sucrose levels in pear

The improvement of fruit quality, in particular sugar content, has been a major goal of plant breeding programmes for many years. Here, 2 varieties of the Ussurian pear (Pyrus ussuriensis), Nanguo, and its high-sucrose accumulation bud sport, Nanhong, were used to study the molecular mechanisms regulating sucrose transport in fruits. Comparative transcriptome analysis showed that in Nanhong fruit, an MYB transcription factor, PuMYB12, and a sucrose transporter protein, PuSUT4-like, were expressed at higher levels, while a paclobutrazol resistance transcription factor, PuPRE6, and a histone deacetylase (HDAC), PuHDAC9-like, were expressed at lower levels in Nanguo fruit. PuSUT4-like silencing and overexpression experiments in Nanguo pear showed that PuSUT4-like is essential for sucrose transportation. PuPRE6 and PuMYB12 act as antagonistic complexes to regulate PuSUT4-like transcription and sucrose accumulation. The histone deacetylation levels of the PuMYB12 and PuSUT4-like promoters were higher in Nanguo fruit than in Nanhong fruit, and Y1H assays showed that HDAC PuHDAC9-like bound directly to the promoters of PuMYB12 and PuSUT4-like. Our results uncovered transcription regulation and epigenetic mechanisms underlying sucrose accumulation in pears.

Transcription factors ABF4 and ABR1 synergistically regulate amylase-mediated starch catabolism in drought tolerance

β-Amylase (BAM)-mediated starch degradation is a main source of soluble sugars that help plants adapt to environmental stresses. Here, we demonstrate that dehydration-induced expression of PtrBAM3 in trifoliate orange (Poncirus trifoliata (L.) Raf.) functions positively in drought tolerance via modulation of starch catabolism. Two transcription factors, PtrABF4 (P. trifoliata abscisic acid-responsive element-binding factor 4) and PtrABR1 (P. trifoliata ABA repressor 1), were identified as upstream transcriptional activators of PtrBAM3 through yeast one-hybrid library screening and protein-DNA interaction assays. Both PtrABF4 and PtrABR1 played a positive role in plant drought tolerance by modulating soluble sugar accumulation derived from BAM3-mediated starch decomposition. In addition, PtrABF4 could directly regulate PtrABR1 expression by binding to its promoter, leading to a regulatory cascade to reinforce the activation of PtrBAM3. Moreover, PtrABF4 physically interacted with PtrABR1 to form a protein complex that further promoted the transcriptional regulation of PtrBAM3. Taken together, our finding reveals that a transcriptional cascade composed of ABF4 and ABR1 works synergistically to upregulate BAM3 expression and starch catabolism in response to drought condition. The results shed light on the understanding of the regulatory molecular mechanisms underlying BAM-mediated soluble sugar accumulation for rendering drought tolerance in plants.

TaERF87 and TaAKS1 synergistically regulate TaP5CS1/TaP5CR1-mediated proline biosynthesis to enhance drought tolerance in wheat

Drought stress limits wheat production and threatens food security world-wide. While ethylene-responsive factors (ERFs) are known to regulate plant response to drought stress, the regulatory mechanisms responsible for a tolerant phenotype remain unclear. Here, we describe the positive regulatory role of TaERF87 in mediating wheat tolerance to drought stress. TaERF87 overexpression (OE) enhances drought tolerance, while silencing leads to drought sensitivity in wheat. RNA sequencing with biochemical assays revealed that TaERF87 activates the expression of the proline biosynthesis genes TaP5CS1 and TaP5CR1 via direct binding to GCC-box elements. Furthermore, proline accumulates to higher levels in TaERF87- and TaP5CS1-OE lines than that in wild-type plants under well-watered and drought stress conditions concomitantly with enhanced drought tolerance in these transgenic lines. Moreover, the interaction between TaERF87 and the bHLH transcription factor TaAKS1 synergistically enhances TaP5CS1 and TaP5CR1 transcriptional activation. TaAKS1 OE also increases wheat drought tolerance by promoting proline accumulation. Additionally, our findings verified that TaERF87 and TaAKS1 are targets of abscisic acid-responsive element binding factor 2 (TaABF2). Together, our study elucidates the mechanisms underlying a positive response to drought stress mediated by the TaABF2-TaERF87/TaAKS1-TaP5CS1/TaP5CR1 module, and identifies candidate genes for the development of elite drought-tolerant wheat varieties.

Identification of ABF/AREB gene family in tomato (Solanum lycopersicum L.) and functional analysis of ABF/AREB in response to ABA and abiotic stresses

Abscisic acid (ABA) is a plant hormone that plays an important regulatory role in plant growth and stress response. The AREB (ABA-responsive element binding protein)/ABF (ABRE-binding factor) are important ABA-signaling components that participate in abiotic stress response. However, genome-scale analysis of ABF/AREB has not been systemically investigated in tomato. This study was conducted to identify tomato ABF/AREB family members and analyze their response to ABA and abiotic stresses. The results show that a total of 10 ABF/AREB members were identified in tomato, which are randomly distributed on five chromosomes. Domain analysis showed that these members exhibit high protein similarity, especially in the basic leucine zipper (bZIP) domain region. Subcellular localization analysis indicated that all 10 ABF/AREB members are localized in the nucleus. Phylogenetic tree analysis showed that tomato ABF/AREB genes are divided into two groups, and they are similar with the orthologs of other plants. The analysis of cis-acting elements showed that most tomato ABF/AREB genes contain a variety of hormones and stress-related elements. Expression profiles of different tissues indicated that SlABF2 and SlABF10 play an important role in fruit ripening. Finally, qRT-PCR analysis revealed that 10 tomato ABF/AREB genes respond to ABA, with SlABF3 being the most sensitive. SlABF3, SlABF5 and SlABF10 positively respond to salt and cold stresses. SlABF1, SlABF3 and SlABF10 are significantly induced under UV radiation treatment. SlABF3 and SlABF5 are significantly induced in osmotic stress. Overall, this study may provide insight into the role of tomato ABF/AREB homologues in plant response to abiotic stresses, which laid a foundation for future functional study of ABF/AREB in tomato.

Transcription Factor SlAREB1 Is Involved in the Antioxidant Regulation under Saline–Alkaline Stress in Tomato

Basic leucine zipper (bZIP) transcription factors of the ABA-responsive element binding factor/ABA-responsive element binding proteins (ABF/AREB) subfamily have been implicated in abscisic acid (ABA) and abiotic stress responses in plants. However, the specific function of ABF/AREB transcription factors under saline–alkaline stress is unclear. Here, we identified four ABF/AREB transcription factors in tomato and found that SlAREB1 strongly responded to both ABA and saline–alkaline stress. To further explore the function of SlAREB1 under saline–alkaline stress, SlAREB1-overexpressing lines were constructed. Compared with wild-type plants, SlAREB1-overexpressing transgenic tomato plants showed reduced malondialdehyde content, increased the relative water content, and alleviated the degradation of chlorophyll under saline–alkaline stress. Importantly, SlAREB1 directly physically interacted with SlMn-SOD, which improved the activity of antioxidant enzymes and increased the scavenging of excess reactive oxygen species. Overall, the overexpression of SlAREB1 increased the antioxidant capacity of the transgenic tomato under saline–alkaline stress.

Identifying the genetic control of salinity tolerance in the bread wheat landrace Mocho de Espiga Branca

Salinity tolerance in bread wheat is frequently reported to be associated with low leaf sodium (Na+) concentrations. However, the Portuguese landrace, Mocho de Espiga Branca, accumulates significantly higher leaf Na+ but has comparable salinity tolerance to commercial bread wheat cultivars. To determine the genetic loci associated with the salinity tolerance of this landrace, an F2 mapping population was developed by crossing Mocho de Espiga Branca with the Australian cultivar Gladius. The population was phenotyped for 19 salinity tolerance subtraits using both non-destructive and destructive techniques. Genotyping was performed using genotyping-by-sequencing (GBS). Genomic regions associated with salinity tolerance were detected on chromosomes 1A, 1D, 4B and 5A for the subtraits of relative and absolute growth rate (RGR, AGR respectively), and on chromosome 2A, 2B, 4D and 5D for Na+, potassium (K+) and chloride (Cl-) accumulation. Candidate genes that encode proteins associated with salinity tolerance were identified within the loci including Na+/H+ antiporters, K+ channels, H+-ATPase, calcineurin B-like proteins (CBLs), CBL-interacting protein kinases (CIPKs), calcium dependent protein kinases (CDPKs) and calcium-transporting ATPase. This study provides a new insight into the genetic control of salinity tolerance in a Na+ accumulating bread wheat to assist with the future development of salt tolerant cultivars.