Overexpression of FTL1/DDF1, an AP2 transcription factor, enhances tolerance to cold, drought, and heat stresses in Arabidopsis thaliana

Employing Genomic Tools to Explore the Molecular Mechanisms behind the Enhancement of Plant Growth and Stress Resilience Facilitated by a Burkholderia Rhizobacterial Strain

The rhizobacterial strain BJ3 showed 16S rDNA sequence similarity to species within the Burkholderia genus. Its complete genome sequence revealed a 97% match with Burkholderia contaminans and uncovered gene clusters essential for plant-growth-promoting traits (PGPTs). These clusters include genes responsible for producing indole acetic acid (IAA), osmolytes, non-ribosomal peptides (NRPS), volatile organic compounds (VOCs), siderophores, lipopolysaccharides, hydrolytic enzymes, and spermidine. Additionally, the genome contains genes for nitrogen fixation and phosphate solubilization, as well as a gene encoding 1-aminocyclopropane-1-carboxylate (ACC) deaminase. The treatment with BJ3 enhanced root architecture, boosted vegetative growth, and accelerated early flowering in Arabidopsis. Treated seedlings also showed increased lignin production and antioxidant capabilities, as well as notably increased tolerance to water deficit and high salinity. An RNA-seq transcriptome analysis indicated that BJ3 treatment significantly activated genes related to immunity induction, hormone signaling, and vegetative growth. It specifically activated genes involved in the production of auxin, ethylene, and salicylic acid (SA), as well as genes involved in the synthesis of defense compounds like glucosinolates, camalexin, and terpenoids. The expression of AP2/ERF transcription factors was markedly increased. These findings highlight BJ3's potential to produce various bioactive metabolites and its ability to activate auxin, ethylene, and SA signaling in Arabidopsis, positioning it as a new Burkholderia strain that could significantly improve plant growth, stress resilience, and immune function.

Modulation of early gene expression responses to water deprivation stress by the E3 ubiquitin ligase ATL80: implications for retrograde signaling interplay

BACKGROUND

Primary response genes play a pivotal role in translating short-lived stress signals into sustained adaptive responses. In this study, we investigated the involvement of ATL80, an E3 ubiquitin ligase, in the dynamics of gene expression following water deprivation stress. We observed that ATL80 is rapidly activated within minutes of water deprivation stress perception, reaching peak expression around 60 min before gradually declining. ATL80, despite its post-translational regulation role, emerged as a key player in modulating early gene expression responses to water deprivation stress.

RESULTS

The impact of ATL80 on gene expression was assessed using a time-course microarray analysis (0, 15, 30, 60, and 120 min), revealing a burst of differentially expressed genes, many of which were associated with various stress responses. In addition, the diversity of early modulation of gene expression in response to water deprivation stress was significantly abolished in the atl80 mutant compared to wild-type plants. A subset of 73 genes that exhibited a similar expression pattern to ATL80 was identified. Among them, several are linked to stress responses, including ERF/AP2 and WRKY transcription factors, calcium signaling genes, MAP kinases, and signaling peptides. Promoter analysis predicts enrichment of binding sites for CAMTA1 and CAMTA5, which are known regulators of rapid stress responses. Furthermore, we have identified a group of differentially expressed ERF/AP2 transcription factors, proteins associated with folding and refolding, as well as pinpointed core module genes which are known to play roles in retrograde signaling pathways that cross-referenced with the early ATL80 transcriptome.

CONCLUSIONS

Based on these findings, we propose that ATL80 may target one or more components within the retrograde signaling pathways for degradation. In essence, ATL80 serves as a bridge connecting these signaling pathways and effectively functions as an alarm signal.

Metabolomics reveal root differential metabolites of different root-type alfalfa under drought stress

Introduction

Alfalfa (Medicago sativa L.) is the favored premium feed ingredient in animal husbandry production which is in serious jeopardy due to soil moisture shortages. It is largely unknown how different root types of alfalfa respond to arid-induced stress in terms of metabolites and phytohormones.

Methods

Therefore, rhizomatous rooted M. sativa 'Qingshui' (or QS), tap-rooted M. sativa 'Longdong' (or LD), and creeping rooted M. varia 'Gannong No. 4' (or GN) were investigated to identify metabolites and phytohormones responses to drought conditions.

Results

We found 164, 270, and 68 significantly upregulated differential metabolites were categorized into 35, 38, and 34 metabolic pathways in QS, LD, and GN within aridity stress, respectively. Amino acids, organic acids, sugars, and alkaloids were the four categories of primary differential metabolites detected, which include 6-gingerol, salicylic acid (SA), indole-3-acetic acid (IAA), gibberellin A4 (GA4), abscisic acid (ABA), trans-cinnamic acid, sucrose, L-phenylalanine, L-tyrosine, succinic acid, and nicotinic acid and so on, turns out these metabolites are essential for the resistance of three root-type alfalfa to aridity coercing.

Discussion

The plant hormone signal transduction (PST) pathway was dramatically enriched after drought stress. IAA and ABA were significantly accumulated in the metabolites, indicating that they play vital roles in the response of three root types of alfalfa to water stress, and QS and LD exhibit stronger tolerance than GN under drought stress.

Involvement of GA3-oxidase in inhibitory effect of nitric oxide on primary root growth in Arabidopsis

Both NO and GAs are essential for regulating various physiological processes and stress responses in plants. However, the interaction between these two molecules remains unclear. We investigated the distinct response patterns of Arabidopsis thaliana Col-0 and GA synthesis functional deficiency mutants to NO by measuring root length. To investigate underlying mechanisms, we detected bioactive GA content using UHPLC-ESI-MS/MS, assessed the accumulation of ROS by chemical staining Arabidopsis roots. We also conducted RNA-seq analysis and compared results between Col-0 and ga3ox1, with and without SNP (as NO donor) treatment. Phenotypic results revealed that the inhibitory effect of NO on primary roots of Arabidopsis was primarily mediated by GA3-oxidase, rather than GA20-oxidase or GA2-oxidase. The content of GA3 decreased in Col-0 treated with SNP, whereas this decrease was not observed in ga3ox1. The deficiency of GA3-oxidase alleviated the buildup of H2 O2 in roots when treated with SNP. We identified 222 DEGs. GO annotation of these DEGs revealed that all top 20 GO terms were related to stress responses. Moreover, three DEGs were annotated to GA-related processes (DDF1, DDF2, EXPA1), and seven DEGs were associated with root development (RAV1, RGF2, ERF71, ZAT6, MYB77, XT1, and DTX50). In summary, NO inhibits primary root growth partially by repressing GA3-oxidase catalysed GA3 synthesis in Arabidopsis. ROS, Ca2+ , DDF1, DDF2, EXPA1 and seven root development-related genes may be involved in crosstalk between NO and GAs.

Exploring the Role of TaPLC1-2B in Heat Tolerance at Seedling and Adult Stages of Wheat through Transcriptome Analysis

Heat stress is a major abiotic stress that can cause serious losses of a crop. Our previous work identified a gene involved in heat stress tolerance in wheat, TaPLC1-2B. To further investigate its mechanisms, in the present study, TaPLC1-2B RNAi-silenced transgenic wheat and the wild type were comparatively analyzed at both the seedling and adult stages, with or without heat stress, using transcriptome sequencing. A total of 15,549 differentially expressed genes (DEGs) were identified at the adult stage and 20,535 DEGs were detected at the seedling stage. After heat stress, an enrichment of pathways such as phytohormones and mitogen-activated protein kinase signaling was mainly found in the seedling stage, and pathways related to metabolism, glycerophospholipid metabolism, circadian rhythms, and ABC transporter were enriched in the adult stage. Auxin and abscisic acid were downregulated in the seedling stage and vice versa in the adult stage; and the MYB, WRKY, and no apical meristem gene families were downregulated in the seedling stage in response to heat stress and upregulated in the adult stage in response to heat stress. This study deepens our understanding of the mechanisms of TaPLC1-2B in regard to heat stress in wheat at the seedling and adult stages.

Genetic dissection of morphological variation between cauliflower and a rapid cycling Brassica oleracea line

To improve resolution to small genomic regions and sensitivity to small-effect loci in the identification of genetic factors conferring the enlarged inflorescence and other traits of cauliflower while also expediting further genetic dissection, 104 near-isogenic introgression lines (NIILs) covering 78.56% of the cauliflower genome, were selected from an advanced backcross population using cauliflower [Brassica oleracea var. botrytis L., mutant for Orange gene (ORG)] as the donor parent and a rapid cycling line (TO1434) as recurrent parent. Subsets of the advanced backcross population and NIILs were planted in the field for 8 seasons, finding 141 marker-trait associations for 15 leaf-, stem-, and flower-traits. Exemplifying the usefulness of these lines, we delineated the previously known flower color gene to a 4.5 MB interval on C3; a gene for small plant size to a 3.4 MB region on C8; and a gene for large plant size and flowering time to a 6.1 MB region on C9. This approach unmasked closely linked QTL alleles with opposing effects (on chr. 8) and revealed both alleles with expected phenotypic effects and effects opposite the parental phenotypes. Selected B. oleracea NIILs with short generation time add new value to widely used research and teaching materials.

Herbaceous peony AP2/ERF transcription factor binds the promoter of the tryptophan decarboxylase gene to enhance high-temperature stress tolerance

Global warming has multifarious adverse effects on plant growth and productivity. Nonetheless, the effects of endogenous phytomelatonin on the high-temperature resistance of plants and the underlying genetic mechanisms remain unclear. Here, herbaceous peony (Paeonia lactiflora Pall.) tryptophan decarboxylase (TDC) gene involved in phytomelatonin biosynthesis was shown to respond to high-temperature stress at the transcriptional level, and its transcript level was positively correlated with phytomelatonin production. Moreover, overexpression of PlTDC enhanced phytomelatonin production and high-temperature stress tolerance in transgenic tobacco, while silencing PlTDC expression decreased these parameters in P. lactiflora. In addition, a 2402 bp promoter fragment of PlTDC was isolated, and DNA pull-down assay revealed that one APETALA2/ethylene-responsive element-binding factor (AP2/ERF) transcription factor, PlTOE3, could specifically activate the PlTDC promoter, which was further verified by yeast one-hybrid assay and luciferase reporter assay. PlTOE3 was a nucleus-localized protein, and its transcript level responded to high-temperature stress. Additionally, transgenic tobacco overexpressing PlTOE3 showed enhanced phytomelatonin production and high-temperature stress tolerance, while silencing PlTDC expression obtained the opposite results. These results illustrated that PlTOE3 bound the PlTDC promoter to enhance high-temperature stress tolerance by increasing phytomelatonin production in P. lactiflora.

Specific CBF transcription factors and cold-responsive genes fine-tune the early triggering response after acquisition of cold priming and memory

Plants need to adapt to fluctuating temperatures throughout their lifetime. Previous research showed that Arabidopsis memorizes a first cold stress (priming) and improves its primed freezing tolerance further when subjected to a second similar stress after a lag phase. This study investigates primary metabolomic and transcriptomic changes during early cold priming or triggering after 3 days at 4°C interrupted by a memory phase. DREB1 family transcription factors DREB1C/CBF2, DREB1D/CBF4, DREB1E/DDF2, and DREB1F/DDF1 were strongly significantly induced throughout the entire triggering. During triggering, genes encoding Late Embryogenesis Abundant (LEA), antifreeze proteins or detoxifiers of reactive oxygen species (ROS) were higher expressed compared with priming. Examples of early triggering responders were xyloglucan endotransglucosylase/hydrolase genes encoding proteins involved in cell wall remodeling, while late responders were identified to act in fine-tuning the stress response and developmental regulation. Induction of non-typical members of the DREB subfamily of ERF/AP2 transcription factors, the relatively small number of induced CBF regulon genes and a slower accumulation of selected cold stress associated metabolites indicate that a cold triggering stimulus might be sensed as milder stress in plants compared with priming. Further, strong induction of CBF4 throughout triggering suggests a unique function of this gene for the response to alternating temperatures.

CPK28-NLP7 module integrates cold-induced Ca2+ signal and transcriptional reprogramming in Arabidopsis

Exposure to cold triggers a spike in cytosolic calcium (Ca²⁺) that often leads to transcriptional reprogramming in plants. However, how this Ca²⁺ signal is perceived and relayed to the downstream cold signaling pathway remains unknown. Here, we show that the CALCIUM-DEPENDENT PROTEIN KINASE 28 (CPK28) initiates a phosphorylation cascade to specify transcriptional reprogramming downstream of cold-induced Ca²⁺ signal. Plasma membrane (PM)-localized CPK28 is activated rapidly upon cold shock within 10 seconds in a Ca²⁺-dependent manner. CPK28 then phosphorylates and promotes the nuclear translocation of NIN-LIKE PROTEIN 7 (NLP7), a transcription factor that specifies the transcriptional reprogramming of cold-responsive gene sets in response to Ca²⁺, thereby positively regulating plant response to cold stress. This study elucidates a previously unidentified mechanism by which the CPK28-NLP7 regulatory module integrates cold-evoked Ca²⁺ signal and transcriptome and thus uncovers a key strategy for the rapid perception and transduction of cold signals from the PM to the nucleus.

Dehydration-Responsive Element Binding Protein 1C, 1E, and 1G Promote Stress Tolerance to Chilling, Heat, Drought, and Salt in Rice

The dehydration-responsive element binding protein 1 (DREB1)/C-repeat-binding factor (CBF) genes are key regulators of cold acclimation and freezing tolerance in the chilling tolerant Arabidopsis thaliana. Here, we investigated the function of three members of the 10 rice DREB1 genes, OsDREB1C, E, and G, in the chilling sensitive rice plants. Their loss of function (LOF) mutants were each more chilling susceptible compared to the wild type, and the LOF mutants of all three genes, dreb1ceg, were more chilling susceptible than any of the single mutants. Strikingly, these mutants were capable of cold acclimation, indicating that these rice DREB1 genes are important for basal chilling tolerance but not cold acclimation. Transcriptome and physiology analyses suggest that the OsDREB1C/E/G genes are involved in reactive oxygen species (ROS) scavenging and cell death regulation under chilling. Furthermore, these three rice DREB1 genes are found to promote tolerance to other abiotic stresses: the OsDREB1C/E/G genes are positive regulators of heat tolerance, OsDREB1C and OsDREB1G are positive regulators of salt tolerance, and OsDREB1G is a positive regulator of drought tolerance. These findings expand our knowledge of the roles of DREB1 proteins in plants, enhance our mechanistic understanding of abiotic stress tolerance and will facilitate the generation of stress-tolerant crop plants.

Overexpression of the Salix matsudana SmAP2-17 gene improves Arabidopsis salinity tolerance by enhancing the expression of SOS3 and ABI5

BACKGROUND

Salix matsudana (Koidz.) is a widely planted ornamental allotetraploid tree species. Genetic engineering can be used to enhance the tolerance of this species to soil salinization, endowing varieties with the ability to grow along coastlines, thereby mitigating afforestation and protecting the environment. The AP2/ERF family of transcription factors (TFs) plays multidimensional roles in plant biotic/abiotic stress tolerance and plant development. In this study, we cloned the SmAP2-17 gene and performed functional analysis of its role in salt tolerance. This study aims to identify key genes for future breeding of stress-resistant varieties of Salix matsudana.

RESULTS

SmAP2-17 was predicted to be a homolog of AP2-like ethylene-responsive transcription factor ANT isoform X2 from Arabidopsis, with a predicted ORF of 2058 bp encoding an estimated protein of 685 amino acids containing two conserved AP2 domains (PF00847.20). SmAP2-17 had a constitutive expression pattern and was localized to the nucleus. The overexpression of the native SmAP2-17 CDS sequence in Arabidopsis did not increase salt tolerance because of the reduced expression level of ectopic SmAP2-17, potentially caused by salt-induced RNAi. Transgenic lines with high expression of optimized SmAP2-17 CDS under salt stress showed enhanced tolerance to salt. Moreover, the expression of general stress marker genes and important salt stress signaling genes, including RD29A, ABI5, SOS3, AtHKT1, and RBohF, were upregulated in SmAP2-17-overexpressed lines, with expression levels consistent with that of SmAP2-17 or optimized SmAP2-17. Promoter activity analysis using dual luciferase analysis showed that SmAP2-17 could bind the promoters of SOS3 and ABI5 to activate their expression, which plays a key role in regulating salt tolerance.

CONCLUSIONS

The SmAP2-17 gene isolated from Salix matsudana (Koidz.) is a positive regulator that improves the resistance of transgenic plants to salt stress by upregulating SOS3 and ABI5 genes. This study provides a potential functional gene resource for future generation of salt-resistant Salix lines by genetic engineering.

Identification of bHLH genes through genome-wide association study and antisense expression of ZjbHLH076/ZjICE1 influence tolerance to low temperature and salinity in Zoysia japonica

Abiotic stress greatly affects plant growth and developmental processes, resulting in poor productivity. A variety of basic helix-loop-helix (bHLH) transcription factors (TFs) that play important roles in plant abiotic stress response pathways have been identified. However, bHLH proteins of Zoysia japonica, one of the warm-season turfgrasses, have not been widely studied. In this study, 141 bHLH genes (ZjbHLHs) were identified and classified into 22 subfamilies. The ZjbHLHs were mapped on 19 chromosomes except for Chr17 and one pair of the tandemly arrayed genes was identified on Chr06. Also, the co-linearity of ZjbHLHs was found to have been driven mostly by segmental duplication events. The subfamily IIIb genes of our present interest, possessed various stress responsive cis-elements in their promoters. ZjbHLH076/ZjICE1, a MYC-type bHLH TF in subfamily IIIb was analyzed by overexpression and its loss-of-function via overexpressing a short ZjbHLH076/ZjICE1 fragment in the antisense direction. The overexpression of ZjbHLH076/ZjICE1 enhanced the tolerance to cold and salinity stress in the transgenic Z. japonica plants. However, the anti-sense expression of ZjbHLH076/ZjICE1 showed sensitive to these abiotic stresses. These results suggest that ZjbHLH076/ZjICE1 would be a promising candidate for the molecular breeding program to improve the abiotic stress tolerance of Z. japonica.

Reproductive Stage Drought Tolerance in Wheat: Importance of Stomatal Conductance and Plant Growth Regulators

Drought stress requires plants to adjust their water balance to maintain tissue water levels. Isohydric plants (‘water-savers’) typically achieve this through stomatal closure, while anisohydric plants (‘water-wasters’) use osmotic adjustment and maintain stomatal conductance. Isohydry or anisohydry allows plant species to adapt to different environments. In this paper we show that both mechanisms occur in bread wheat (Triticum aestivum L.). Wheat lines with reproductive drought-tolerance delay stomatal closure and are temporarily anisohydric, before closing stomata and become isohydric at higher threshold levels of drought stress. Drought-sensitive wheat is isohydric from the start of the drought treatment. The capacity of the drought-tolerant line to maintain stomatal conductance correlates with repression of ABA synthesis in spikes and flag leaves. Gene expression profiling revealed major differences in the drought response in spikes and flag leaves of both wheat lines. While the isohydric drought-sensitive line enters a passive growth mode (arrest of photosynthesis, protein translation), the tolerant line mounts a stronger stress defence response (ROS protection, LEA proteins, cuticle synthesis). The drought response of the tolerant line is characterised by a strong response in the spike, displaying enrichment of genes involved in auxin, cytokinin and ethylene metabolism/signalling. While isohydry may offer advantages for longer term drought stress, anisohydry may be more beneficial when drought stress occurs during the critical stages of wheat spike development, ultimately improving grain yield.

Overexpression of a carrot BCH gene, DcBCH1, improves tolerance to drought in Arabidopsis thaliana

BACKGROUND

Carrot (Daucus carota L.), an important root vegetable, is very popular among consumers as its taproot is rich in various nutrients. Abiotic stresses, such as drought, salt, and low temperature, are the main factors that restrict the growth and development of carrots. Non-heme carotene hydroxylase (BCH) is a key regulatory enzyme in the β-branch of the carotenoid biosynthesis pathway, upstream of the abscisic acid (ABA) synthesis pathway.

RESULTS

In this study, we characterized a carrot BCH encoding gene, DcBCH1. The expression of DcBCH1 was induced by drought treatment. The overexpression of DcBCH1 in Arabidopsis thaliana resulted in enhanced tolerance to drought, as demonstrated by higher antioxidant capacity and lower malondialdehyde content after drought treatment. Under drought stress, the endogenous ABA level in transgenic A. thaliana was higher than that in wild-type (WT) plants. Additionally, the contents of lutein and β-carotene in transgenic A. thaliana were lower than those in WT, whereas the expression levels of most endogenous carotenogenic genes were significantly increased after drought treatment.

CONCLUSIONS

DcBCH1 can increase the antioxidant capacity and promote endogenous ABA levels of plants by regulating the synthesis rate of carotenoids, thereby regulating the drought resistance of plants. These results will help to provide potential candidate genes for plant drought tolerance breeding.

Convergence and Divergence: Signal Perception and Transduction Mechanisms of Cold Stress in Arabidopsis and Rice

Cold stress, including freezing stress and chilling stress, is one of the major environmental factors that limit the growth and productivity of plants. As a temperate dicot model plant species, Arabidopsis develops a capability to freezing tolerance through cold acclimation. The past decades have witnessed a deep understanding of mechanisms underlying cold stress signal perception, transduction, and freezing tolerance in Arabidopsis. In contrast, a monocot cereal model plant species derived from tropical and subtropical origins, rice, is very sensitive to chilling stress and has evolved a different mechanism for chilling stress signaling and response. In this review, the authors summarized the recent progress in our understanding of cold stress response mechanisms, highlighted the convergent and divergent mechanisms between Arabidopsis and rice plasma membrane cold stress perceptions, calcium signaling, phospholipid signaling, MAPK cascade signaling, ROS signaling, and ICE-CBF regulatory network, as well as light-regulated signal transduction system. Genetic engineering approaches of developing freezing tolerant Arabidopsis and chilling tolerant rice were also reviewed. Finally, the future perspective of cold stress signaling and tolerance in rice was proposed.

AP2/ERF, an important cold stress-related transcription factor family in plants: A review

Increasing the vulnerability of plants especially crops to a wide range of cold stress reduces plant growth, development, yield production, and plant distribution. Cold stress induces physiological, morphological, biochemical, phenotypic, and molecular changes in plants. Transcription factor (TF) is one of the most important regulators that mediate gene expression. TF is activated by the signal transduction pathway, together with cis-acting element modulate the transcription of cold-responsive genes which contribute to increasing cold tolerance in plants. Here, AP2/ERF TF family is one of the most important cold stress-related TF families that along with other TF families, such as WRKY, bHLH, bZIP, MYB, NAC, and C2H2 interrelate to enhance cold stress tolerance. Over the past decade, significant progress has been found to solve the role of transcription factors (TFs) in improving cold tolerance in plants, such as omics analysis. Furthermore, numerous studies have identified and characterized the complexity of cold stress mechanisms among TFs or between TFs and other factors (endogenous and exogenous) including phytohormones, eugenol, and light. The role, function, and relationship among these TFs or between TFs and other factors to enhance cold tolerance still need to be clarified. Here, the current study analysed the role of AP2/ERF TF and the linkages among AP2/ERF with MYB, WRKY, bZIP, bHLH, C2H2, or NAC against cold stress tolerance.

BrPP5.2 Overexpression Confers Heat Shock Tolerance in Transgenic Brassica rapa through Inherent Chaperone Activity, Induced Glucosinolate Biosynthesis, and Differential Regulation of Abiotic Stress Response Genes

Plant phosphoprotein phosphatases are ubiquitous and multifarious enzymes that respond to developmental requirements and stress signals through reversible dephosphorylation of target proteins. In this study, we investigated the hitherto unknown functions of Brassica rapa protein phosphatase 5.2 (BrPP5.2) by transgenic overexpression of B. rapa lines. The overexpression of BrPP5.2 in transgenic lines conferred heat shock tolerance in 65–89% of the young transgenic seedlings exposed to 46 °C for 25 min. The examination of purified recombinant BrPP5.2 at different molar ratios efficiently prevented the thermal aggregation of malate dehydrogenase at 42 °C, thus suggesting that BrPP5.2 has inherent chaperone activities. The transcriptomic dynamics of transgenic lines, as determined using RNA-seq, revealed that 997 and 1206 (FDR < 0.05, logFC ≥ 2) genes were up- and down-regulated, as compared to non-transgenic controls. Statistical enrichment analyses revealed abiotic stress response genes, including heat stress response (HSR), showed reduced expression in transgenic lines under optimal growth conditions. However, most of the HSR DEGs were upregulated under high temperature stress (37 °C/1 h) conditions. In addition, the glucosinolate biosynthesis gene expression and total glucosinolate content increased in the transgenic lines. These findings provide a new avenue related to BrPP5.2 downstream genes and their crucial metabolic and heat stress responses in plants.

Genome-wide identification and expression analysis of the AT-hook Motif Nuclear Localized gene family in soybean

BACKGROUND

Soybean is an important legume crop and has significant agricultural and economic value. Previous research has shown that the AT-Hook Motif Nuclear Localized (AHL) gene family is highly conserved in land plants, playing crucial roles in plant growth and development. To date, however, the AHL gene family has not been studied in soybean.

RESULTS

To investigate the roles played by the AHL gene family in soybean, genome-wide identification, expression patterns and gene structures were performed to analyze. We identified a total of 63 AT-hook motif genes, which were characterized by the presence of the AT-hook motif and PPC domain in soybean. The AT-hook motif genes were distributed on 18 chromosomes and formed two distinct clades (A and B), as shown by phylogenetic analysis. All the AHL proteins were further classified into three types (I, II and III) based on the AT-hook motif. Type-I was belonged to Clade-A, while Type-II and Type-III were belonged to Clade-B. Our results also showed that the main type of duplication in the soybean AHL gene family was segmented duplication event. To discern whether the AHL gene family was involved in stress response in soybean, we performed cis-acting elements analysis and found that AHL genes were associated with light responsiveness, anaerobic induction, MYB and gibberellin-responsiveness elements. This suggest that AHL genes may participate in plant development and mediate stress response. Moreover, a co-expression network analysis showed that the AHL genes were also involved in energy transduction, and the associated with the gibberellin pathway and nuclear entry signal pathways in soybean. Transcription analysis revealed that AHL genes in Jack and Williams82 have a common expression pattern and are mostly expressed in roots, showing greater sensitivity under drought and submergence stress. Hence, the AHL gene family mainly reacts on mediating stress responses in the roots and provide comprehensive information for further understanding of the AT-hook motif gene family-mediated stress response in soybean.

CONCLUSION

Sixty-three AT-hook motif genes were identified in the soybean genome. These genes formed into two distinct phylogenetic clades and belonged to three different types. Cis-acting elements and co-expression network analyses suggested that AHL genes participated in significant biological processes. This work provides important theoretical basis for the understanding of AHLs biological functions in soybean.

Overexpression of the Zygophyllum xanthoxylum Aquaporin, ZxPIP1;3, Promotes Plant Growth and Stress Tolerance

Drought and salinity can result in cell dehydration and water unbalance in plants, which seriously diminish plant growth and development. Cellular water homeostasis maintained by aquaporin is one of the important strategies for plants to cope with these two stresses. In this study, a stress-induced aquaporin, ZxPIP1;3, belonging to the PIP1 subgroup, was identified from the succulent xerophyte Zygophyllum xanthoxylum. The subcellular localization showed that ZxPIP1;3-GFP was located in the plasma membrane. The overexpression of ZxPIP1;3 in Arabidopsis prompted plant growth under favorable condition. In addition, it also conferred salt and drought tolerance with better water status as well as less ion toxicity and membrane injury, which led to more efficient photosynthesis and improved growth vigor via inducing stress-related responsive genes. This study reveals the molecular mechanisms of xerophytes’ stress tolerance and provides a valuable candidate that could be used in genetic engineering to improve crop growth and stress tolerance.

The transcription factor WRKY22 is required during cryo-stress acclimation in Arabidopsis shoot tips

Storage of meristematic tissue at ultra-low temperatures offers a mean to maintain valuable genetic resources from vegetatively reproduced plants. To reveal the biology underlying cryo-stress, shoot tips of the model plant Arabidopsis thaliana were subjected to a standard preservation procedure. A transcriptomic approach was taken to describe the subsequent cellular events which occurred. The cryoprotectant treatment induced the changes in the transcript levels of genes associated with RNA processing and primary metabolism. Explants of a mutant lacking a functional copy of the transcription factor WRKY22 were compromised for recovery. A number of putative downstream targets of WRKY22 were identified, some related to phytohormone-mediated defense, to the osmotic stress response, and to development. There were also alterations in the abundance of transcript produced by genes encoding photosynthesis-related proteins. The wrky22 mutant plants developed an open stomata phenotype in response to their exposure to the cryoprotectant solution. WRKY22 probably regulates a transcriptional network during cryo-stress, linking the explant's defense and osmotic stress responses to changes in its primary metabolism. A model is proposed linking WRKY53 and WRKY70 downstream of the action of WRKY22.

The cis-regulatory codes of response to combined heat and drought stress in Arabidopsis thaliana

Plants respond to their environment by dynamically modulating gene expression. A powerful approach for understanding how these responses are regulated is to integrate information about cis-regulatory elements (CREs) into models called cis-regulatory codes. Transcriptional response to combined stress is typically not the sum of the responses to the individual stresses. However, cis-regulatory codes underlying combined stress response have not been established. Here we modeled transcriptional response to single and combined heat and drought stress in Arabidopsis thaliana. We grouped genes by their pattern of response (independent, antagonistic and synergistic) and trained machine learning models to predict their response using putative CREs (pCREs) as features (median F-measure = 0.64). We then developed a deep learning approach to integrate additional omics information (sequence conservation, chromatin accessibility and histone modification) into our models, improving performance by 6.2%. While pCREs important for predicting independent and antagonistic responses tended to resemble binding motifs of transcription factors associated with heat and/or drought stress, important synergistic pCREs resembled binding motifs of transcription factors not known to be associated with stress. These findings demonstrate how in silico approaches can improve our understanding of the complex codes regulating response to combined stress and help us identify prime targets for future characterization.

VcMYB4a, an R2R3-MYB transcription factor from Vaccinium corymbosum, negatively regulates salt, drought, and temperature stress

MYB transcription factors (TFs) play important roles in the plant's response to abiotic stress. In this study, we cloned a novel MYB TF gene from Vaccinium corymbosum (blueberry) using rapid amplification of cDNA ends (RACE). The cDNA contained a 798-bp open reading frame that encodes a 265-amino acid protein. VcMYB4a possessed a C2/EAR-repressor motif domain and phylogenetic analysis showed that it clustered into a subgroup 4 with six Arabidopsis thaliana MYBs. Quantitative RT-PCR analysis demonstrated that VcMYB4a expression was downregulated by salt, drought, and cold treatment, but was induced by freezing and heat. Overexpression of VcMYB4a in blueberry callus enhanced sensitivity to salt, drought, cold, freezing, and heat stress. These results indicate that VcMYB4a may be an important repressor of abiotic stress in blueberry.

Molecular cloning and functional analysis of lotus salt-induced NnDREB2C, NnPIP1-2 and NnPIP2-1 in Arabidopsis thaliana

Dehydration-responsive element bindings transcription factor (DREBs) and plasma membrane intrinsic proteins (PIPs) have been characterized multi-functions in plant growth and metabolism, as well as in the adaptation to various stresses. In this study, we cloned the full-length cDNA of NnDREB2C from a salt-tolerated lotus species with RT-PCR methods. Analysis of qRT-PCR demonstrated that NnDREB2C mRNA in the leaf dramatically increased after the treatments of NaCl, abscisic acid, low temperature and mannitol. Next, NnDREB2C was cloned into constitutive expression vector pSN1301, which in turn transformed into Arabidopsis thaliana to investigate its function in plants. NnDREB2C overexpression significantly elevated Arabidopsis tolerance against salt and drought stresses, showing higher survival rates, lower conductivity and more chlorophyll content than those of wild-type plants. Moreover, higher germination rates were observed in the NnDREB2C overproducing plants when subjected into the stresses of NaCl and mannitol. Furthermore, we investigate the potential down-stream genes regulated by NnDREB2C and observed a significant increase in expressions of several genes belonging to PIPs family, including PIP1-1, PIP1-2, PIP1-3, PIP1-4 and PIP1-5. Consistently, overexpressed NnPIP1-2 and NnPIP2-1 conferred Arabidopsis the tolerance to stresses. Taken together, we concluded that overexpression of NnDREB2C enhanced the tolerance of salt and drought stresses in plants, which might probably be derived from the increased expression of the genes belonging to PIPs family.

Genome-Wide Identification and Expression Profiling of the ERF Gene Family in Medicago sativa L. Under Various Abiotic Stresses

The AP2/ERF (APETALA2/ETHYLENE RESPONSE FACTOR) transcription factor represents one of the largest plant-specific transcriptional regulators in plants. ERF plays important roles in the regulation of various developmental processes and acts as a mediator in plant external stress responses. However, the research of the ERF gene family is still limited in alfalfa (Medicago sativa L.), one of the most important forage legume species in the world. In the present study, a total of 159 ERF genes were identified, and the phylogenetic reconstruction, classification, conserved motifs, signal peptide prediction, and expression patterns under salt, drought, and low-temperature stresses of these ERF genes were comprehensively analyzed. The ERF genes family in alfalfa could be classified into 10 groups and predicted to be strongly homologous. Based on the structure and functions relationships, the III and IV subfamilies were more likely to play functions in abiotic stresses and 18 MsERF genes were selected for further quantitative real-time PCR validation in different stresses treatment. The results showed that all these MsERF genes were upregulated under three stresses except MsERF008. This study identified the possibility of abiotic tolerance candidate genes playing various roles in stress resistance at the whole-genome level, which would provide primary understanding for exploring ERF-mediated tolerance in alfalfa.

Angiosperm-Wide and Family-Level Analyses of AP2/ERF Genes Reveal Differential Retention and Sequence Divergence After Whole-Genome Duplication

Plants are immobile and often face stressful environmental conditions, prompting the evolution of genes regulating environmental responses. Such evolution is achieved largely through gene duplication and subsequent divergence. One of the most important gene families involved in regulating plant environmental responses and development is the AP2/ERF superfamily; however, the evolutionary history of these genes is unclear across angiosperms and in major angiosperm families adapted to various ecological niches. Specifically, the impact on gene copy number of whole-genome duplication events occurring around the time of the origins of several plant families is unknown. Here, we present the first angiosperm-wide comparative study of AP2/ERF genes, identifying 75 Angiosperm OrthoGroups (AOGs), each derived from an ancestral angiosperm gene copy. Among these AOGs, 21 retain duplicates with increased copy number in many angiosperm lineages, while the remaining 54 AOGs tend to maintain low copy number. Further analyses of multiple species in the Brassicaceae family indicated that family-specific duplicates experienced differential selective pressures in coding regions, with some paralogs showing signs of positive selection. Further, cis regulatory elements also exhibit extensive divergence between duplicates in Arabidopsis. Moreover, comparison of expression levels suggested that AP2/ERF genes with frequently retained duplicates are enriched for broad expression patterns, offering increased opportunities for functional diversification via changes in expression patterns, and providing a mechanism for repeated duplicate retention in some AOGs. Our results represent the most comprehensive evolutionary history of the AP2/ERF gene family, and support the hypothesis that AP2/ERF genes with broader expression patterns are more likely to be retained as duplicates than those with narrower expression profiles, which could lead to a higher chance of duplicate gene subfunctionalization. The greater tendency of some AOGs to retain duplicates, allowing expression and functional divergence, may facilitate the evolution of complex signaling networks in response to new environmental conditions.

VcRR2 regulates chilling-mediated flowering through expression of hormone genes in a transgenic blueberry mutant

The molecular mechanism underlying dormancy release and the induction of flowering remains poorly understood in woody plants. Mu-legacy is a valuable blueberry mutant, in which a transgene insertion caused increased expression of a RESPONSE REGULATOR 2-like gene (VcRR2). Mu-legacy plants, compared with nontransgenic 'Legacy' plants, show dwarfing, promotion of flower bud formation, and can flower under nonchilling conditions. We conducted transcriptomic comparisons in leaves, chilled and nonchilled flowering buds, and late-pink buds, and analyzed a total of 41 metabolites of six groups of hormones in leaf tissues of both Mu-legacy and 'Legacy' plants. These analyses uncovered that increased VcRR2 expression promotes the expression of a homolog of Arabidopsis thaliana ENT-COPALYL DIPHOSPHATE SYNTHETASE 1 (VcGA1), which induces new homeostasis of hormones, including increased gibberellin 4 (GA4) levels in Mu-legacy leaves. Consequently, increased expression of VcRR2 and VcGA1, which function in cytokinin responses and gibberellin synthesis, respectively, initiated the reduction in plant height and the enhancement of flower bud formation of the Mu-legacy plants through interactions of multiple approaches. In nonchilled flower buds, 29 differentially expressed transcripts of 17 genes of five groups of hormones were identified in transcriptome comparisons between Mu-legacy and 'Legacy' plants, of which 22 were chilling responsive. Thus, these analyses suggest that increased expression of VcRR2 was collectively responsible for promoting flower bud formation in highbush blueberry under nonchilling conditions. We report here for the first time the importance of VcRR2 to induce a suite of downstream hormones that promote flowering in woody plants.

Proteomic Responses Under Cold Stress Reveal Unique Cold Tolerance Mechanisms in the Pacific White Shrimp (Litopenaeus vannamei)

The Pacific white shrimp (Litopenaeus vannamei), one of the most widely cultured shrimp species in the world, often suffers from cold stress. To understand the molecular mechanism of cold tolerance in Pacific white shrimp, we conducted a proteomic analysis on two contrasting shrimp cultivars, namely, cold-tolerant Guihai2 (GH2) and cold-sensitive Guihai1 (GH1), under normal temperature (28°C), under cold stress (16°C), and during recovery to 28°C. In total, 3,349 proteins were identified, among which 2,736 proteins were quantified. Based on gene ontology annotations, differentially expressed proteins largely belonged to biological processes, cellular components, and molecular functions. KEGG pathway annotations indicated that the main changes were observed in the lysosome, ribosomes, and oxidative phosphorylation. Subcellular localization analysis showed a significant increase in proteins present in cytosol, extracellular regions, and mitochondria. Combining enrichment-based clustering analysis and qRT-PCR analysis, we found that glutathione S-transferase, zinc proteinase, m7GpppX diphosphatase, AP2 transcription complex, and zinc-finger transcription factors played a major role in the cold stress response in Pacific white shrimp. Moreover, structure proteins, including different types of lectin and DAPPUDRAFT, were indispensable for cold stress tolerance of the Pacific white shrimp. Results indicate the molecular mechanisms of the Pacific white shrimp in response to cold stress and provide new insight into breeding new cultivars with increased cold tolerance.

Overexpression of Zinc Finger Transcription Factor ZAT6 Enhances Salt Tolerance

The purpose of the present investigation is to examine the function of the C2H2-type zinc finger transcription factor of Arabidopsis thaliana 6 (ZAT6) in salt stress tolerance in cells of rice (Oryza sativa L.), cotton (Gossypium hirsutum L.) and slash pine (Pinus elliottii Engelm.). Cells of O. sativa, G. hirsutum, and P. elliottii overexpressing ZAT6 were generated using Agrobacterium-mediated genetic transformation. Molecular and functional analysis of transgenic cell lines demonstrate that overexpression of ZAT6 increased tolerance to salt stress by decreasing lipid peroxidation and increasing the content of abscisic acid (ABA) and GA₈, as well as enhancing the activities of antioxidant enzymes such as ascorbate peroxidise (APOX), catalase (CAT), glutathione reductase (GR), and superoxide dismutase (SOD). In rice cells, ZAT6 also increased expression of Ca²⁺-dependent protein kinase genes OsCPK9 and OsCPK25 by 5–7 fold under NaCl stress. Altogether, our results suggest that overexpression of ZAT6 enhanced salt stress tolerance by increasing antioxidant enzyme activity, hormone content and expression of Ca²⁺-dependent protein kinase in transgenic cell lines of different plant species.

Low doses of triazine xenobiotics mobilize ABA and cytokinin regulations in a stress- and low-energy-dependent manner

The extent of residual contaminations of pesticides through drift, run-off and leaching is a potential threat to non-target plant communities. Arabidopsis thaliana responds to low doses of the herbicide atrazine, and of its degradation products, desethylatrazine and hydroxyatrazine, not only in the long term, but also under conditions of short-term exposure. In order to investigate underlying molecular mechanisms of low-dose responses and to decipher commonalities and specificities between different chemical treatments, parallel transcriptomic studies of the early effects of the atrazine-desethylatrazine-hydroxyatrazine chemical series were undertaken using whole-genome microarrays. All of the triazines under study produced coordinated and specific changes in gene expression. Hydroxyatrazine-responsive genes were mainly linked to root development, whereas atrazine and desethylatrazine mostly affected molecular signaling networks implicated in stress and hormone responses. Analysis of signaling-related genes, promoter sites and shared-function interaction networks highlighted the involvement of energy-, stress-, abscisic acid- and cytokinin-regulated processes, and emphasized the importance of cold-, heat- and drought-related signaling in the perception of low doses of triazines. These links between low-dose xenobiotic impacts and stress-hormone crosstalk pathways give novel insights into plant-pesticide interactions and plant-pollution interactions that are essential for toxicity evaluation in the context of environmental risk assessment.

Transcriptome profile of NO-induced Arabidopsis transcription factor genes suggests their putative regulatory role in multiple biological processes

TFs are important proteins regulating plant responses during environmental stresses. These insults typically induce changes in cellular redox tone driven in part by promoting the production of reactive nitrogen species (RNS). The main source of these RNS is nitric oxide (NO), which serves as a signalling molecule, eliciting defence and resistance responses. To understand how these signalling molecules regulate key biological processes, we performed a large scale S-nitrosocysteine (CySNO)-mediated RNA-seq analysis. The DEGs were analysed to identify potential regulatory TFs. We found a total of 673 (up- and down-regulated) TFs representing a broad range of TF families. GO-enrichment and MapMan analysis suggests that more than 98% of TFs were mapped to the Arabidopsis thaliana genome and classified into pathways like hormone signalling, protein degradation, development, biotic and abiotic stress, etc. A functional analysis of three randomly selected TFs, DDF1, RAP2.6, and AtMYB48 identified a regulatory role in plant growth and immunity. Loss-of-function mutations within DDF1 and RAP2.6 showed compromised basal defence and effector triggered immunity, suggesting their positive role in two major plant defence systems. Together, these results imply an important data representing NO-responsive TFs that will help in exploring the core mechanisms involved in biological processes in plants.

Improving Salt Tolerance of Chickpea Using Modern Genomics Tools and Molecular Breeding

INTRODUCTION

The high protein value, essential minerals, dietary fibre and notable ability to fix atmospheric nitrogen make chickpea a highly remunerative crop, particularly in low-input food production systems. Of the variety of constraints challenging chickpea productivity worldwide, salinity remains of prime concern owing to the intrinsic sensitivity of the crop. In view of the projected expansion of chickpea into arable and salt-stressed land by 2050, increasing attention is being placed on improving the salt tolerance of this crop. Considerable effort is currently underway to address salinity stress and substantial breeding progress is being made despite the seemingly highly-complex and environment-dependent nature of the tolerance trait.

CONCLUSION

This review aims to provide a holistic view of recent advances in breeding chickpea for salt tolerance. Initially, we focus on the identification of novel genetic resources for salt tolerance via extensive germplasm screening. We then expand on the use of genome-wide and cost-effective techniques to gain new insights into the genetic control of salt tolerance, including the responsive genes/QTL(s), gene(s) networks/cross talk and intricate signalling cascades.

A Functional Genomic Perspective on Drought Signalling and its Crosstalk with Phytohormone-mediated Signalling Pathways in Plants

INTRODUCTION

Drought stress is one of the most important abiotic stresses that negatively influence crop performance and productivity. Plants acclimatize to drought stress conditions through altered molecular, biochemical and physiological responses. Gene and/or protein expression and regulation are thought to be modulated upon stress perception and signal transduction for providing requisite endurance to plants.Plant growth regulators or phytohormones are important molecules required for various biological processes in plants and are also central to stress signalling pathways. Among various phytohormones, Abscisic Acid (ABA) and Ethylene (ET) are considered to be the most vital growth regulators implicated in drought stress signalling and tolerance. Besides the above two known classical phytohormones, Salicylic Acid (SA) and Jasmonic Acid (JA) have also been found to potentially enhance abiotic stress tolerance particularly that of drought, salinity, and heat stress tolerance in plants. Apart from these several other growth regulators such as Cytokinins (CKs), Auxin (AUX), Gibberellic Acid (GA), Brassinosteroids (BRs) and Strigolactones (SLs) have also been reported to actively participate in abiotic stress responses and tolerance in plants. The abiotic stress signalling in plants regulated by these hormones further depends upon the nature, intensity, and duration of exposure to various environmental stresses. It has been reported that all these phytohormones are also involved in extensive crosstalk and signal transduction among themselves and/or with other factors.

CONCLUSION

This review thus summarizes the molecular mechanism of drought signalling and its crosstalk with various phytohormone signalling pathways implicated in abiotic stress response and tolerance.

Identification and functional prediction of stress responsive AP2/ERF transcription factors in Brassica napus by genome-wide analysis

Using homology and domain authentication, 321 putative AP2/ERF transcription factors were identified in Brassica napus, called BnAP2/ERF TFs. BnAP2/ERF TFs were classified into five major subfamilies, including DREB, ERF, AP2, RAV, and BnSoloist. This classification is based on phylogenetic analysis, motif identification, gene structure analysis, and physiochemical characterization. These TFs were annotated based on phylogenetic relationship with Brassica rapa. BnAP2/ERF TFs were located on 19 chromosomes of B. napus. Orthologs and paralogs were identified using synteny-based methods Ks calculation within B. napus genome and between B. napus with other species such as B. rapa, Brassica oleracea, and Arabidopsis thaliana indicated that BnAP2/ERF TFs were formed through duplication events occurred before B. napus formation. Kn/Ks values were between 0 and 1, suggesting the purifying selection among BnAP2/ERF TFs. Gene ontology annotation, cis-regulatory elements and functional interaction networks suggested that BnAP2/ERF TFs participate in response to stressors, including drought, high salinity, heat and cold as well as developmental processes particularly organ specification and embryogenesis. The identified cis-regulatory elements in the upstream of BnAP2/ERF TFs were responsive to abscisic acid. Analysis of the expression data derived from Illumina Hiseq 2000 RNA sequencing revealed that BnAP2/ERF genes were highly expressed in the roots comparing to flower buds, leaves, and stems. Also, the ERF subfamily was over-expressed under salt and fungal treatments. BnERF039 and BnERF245 are candidates for salt-tolerant B. napus. BnERF253-256 and BnERF260-277 are potential cytokinin response factors. BnERF227, BnERF228, BnERF234, BnERF134, BnERF132, BnERF176, and BnERF235 were suggested for resistance against Leptosphaeria maculan and Leptosphaeria biglobosa.

Transcriptomic changes reveal gene networks responding to the overexpression of a blueberry DWARF AND DELAYED FLOWERING 1 gene in transgenic blueberry plants

BACKGROUND

Constitutive expression of the CBF/DREB1 for increasing freezing tolerance in woody plants is often associated with other phenotypic changes including dwarf plant and delayed flowering. These phenotypic changes have been observed when Arabidopsis DWARF AND DELAYED FLOWERING 1 (DDF1) was overexpressed in A. thaliana plants. To date, the DDF1 orthologues have not been studied in woody plants. The aim of this study is to investigate transcriptomic responses to the overexpression of blueberry (Vaccinium corymbosum) DDF1 (herein, VcDDF1-OX).

RESULTS

The VcDDF1-OX resulted in enhanced freezing tolerance in tetraploid blueberry plants and did not result in significant changes in plant size, chilling requirement, and flowering time. Comparative transcriptome analysis of transgenic 'Legacy-VcDDF1-OX' plants containing an overexpressed VcDDF1 with non-transgenic highbush blueberry 'Legacy' plants revealed the VcDDF1-OX derived differentially expressed (DE) genes and transcripts in the pathways of cold-response, plant flowering, DELLA proteins, and plant phytohormones. The increase in freezing tolerance was associated to the expression of cold-regulated genes (CORs) and the ethylene pathway genes. The unchanged plant size, dormancy and flowering were due to the minimal effect of the VcDDF1-OX on the expression of DELLA proteins, flowering pathway genes, and the other phytohormone genes related to plant growth and development. The DE genes in auxin and cytokinin pathways suggest that the VcDDF1-OX has also altered plant tolerance to drought and high salinity.

CONCLUSION

A DDF1 orthologue in blueberry functioned differently from the DDF1 reported in Arabidopsis. The overexpression of VcDDF1 or its orthologues is a new approach to increase freezing tolerance of deciduous woody plant species with no obvious effect on plant size and plant flowering time.

Cassava C-repeat binding factor 1 gene responds to low temperature and enhances cold tolerance when overexpressed in Arabidopsis and cassava

Cassava MeCBF1 is a typical CBF transcription factor mediating cold responses but its low expression in apical buds along with a retarded response cause inefficient upregulation of downstream cold-related genes, rendering cassava chilling-sensitive. Low temperature is a major abiotic stress factor affecting survival, productivity and geographic distribution of important crops worldwide. The C-repeat/dehydration-responsive element binding transcription factors (CBF/DREB) are important regulators of abiotic stress response in plants. In this study, MeCBF1, a CBF-like gene, was identified in the tropical root crop cassava (Manihot esculenta Crantz). The MeCBF1 encodes a protein that shares strong homology with DREB1As/CBFs from Arabidopsis as well as other species. The MeCBF1 was localized to the nucleus and is mainly expressed in stem and mature leaves, but not in apical buds or stem cambium. MeCBF1 expression was not only highly responsive to cold, but also significantly induced by salt, PEG and ABA treatment. Several stress-associated cis-elements were found in its promoter region, e.g., ABRE-related, MYC recognition sites, and MYB responsive element. Compared with AtCBF1, the MeCBF1 expression induced by cold in cassava was retarded and upregulated only after 4 h, which was also confirmed by its promoter activity. Overexpression of MeCBF1 in transgenic Arabidopsis and cassava plants conferred enhanced crytolerance. The CBF regulon was smaller and not entirely co-regulated with MeCBF1 expression in overexpressed cassava. The retarded MeCBF1 expression in response to cold and attenuated CBF-regulon might lead cassava to chilling sensitivity.

The Arabidopsis UGT87A2, a stress-inducible family 1 glycosyltransferase, is involved in the plant adaptation to abiotic stresses

Glycosyltransferase (GT) family-1, the biggest GT family in plants, typically participates in modification of small molecules and affects many aspects during plant development. In Arabidopsis thaliana, although some UDP glycosyltransferases (UGTs) of family-1 have been functionally characterized, functions of most the UGTs remain unknown or fragmentary. Here, we report data for the Arabidopsis UGT87A2, a stress-regulated GT. We found that UGT87A2 could be dramatically induced by salinity, osmotic stress, drought and ABA. Overexpression of UGT87A2 (87A2OE) leads to accelerated germination and greening, higher survival rate as well as increased root length against abiotic stresses compared with those of wild-type (WT) plants. In addition, we observed lower water loss rate in the 87A2OE plants due to smaller stomatal apertures. The transgenic plants also showed reduced levels of H₂ O₂ and superoxide under low water status compared with those of WT plants. Consistently, function loss of UGT87A2 in ugt87a2 knockout lines resulted in opposite performances under these conditions. A transcriptome profiling revealed that 121 genes were differentially regulated upon UGT87A2 overexpression, and a large number of stress-induced genes were upregulated in UGT87A2 overexpression plants. Expression of seven genes among them were assessed by quantitative real-time polymerase chain reaction (qRT-PCR), including CPK32, CYP81F2, MYB96, DREB2A, FBS1, PUB23 and RAV2 under both control and stress treatments, and the results greatly validated our transcriptome data. Taken together, our findings support an explicit role of UGT87A2 in adaptation to abiotic stresses.

Expansion and stress responses of the AP2/EREBP superfamily in cotton

Background

The allotetraploid cotton originated from one hybridization event between an extant progenitor of Gosssypium herbaceum (A₁) or G. arboreum (A₂) and another progenitor, G. raimondii Ulbrich (D₅) 1–1.5 million years ago (Mya). The APETALA2/ethylene-responsive element binding protein (AP2/EREBP) transcription factors constitute one of the largest and most conserved gene families in plants. They are characterized by their AP2 domain, which comprises 60–70 amino acids, and are classified into four main subfamilies: the APETALA2 (AP2), Related to ABI3/VP1 (RAV), Dehydration-Responsive Element Binding protein (DREB) and Ethylene-Responsive Factor (ERF) subfamilies. The AP2/EREBP genes play crucial roles in plant growth, development and biotic and abiotic stress responses. Hence, understanding the molecular characteristics of cotton stress tolerance and gene family expansion would undoubtedly facilitate cotton resistance breeding and evolution research.

Results

A total of 269 AP2/EREBP genes were identified in the G. raimondii (D5) cotton genome. The protein domain architecture and intron/exon structure are simple and relatively conserved within each subfamily. They are distributed throughout all chromosomes but are clustered on various chromosomes due to genomic tandem duplication. We identified 73 tandem duplicated genes and 221 segmental duplicated gene pairs which contributed to the expansion of AP2/EREBP superfamily. Of them, tandem duplication was the most important force of the expansion of the B3 group. Transcriptome analysis showed that 504 AP2/EREBP genes were expressed in at least one tested G. hirsutum TM-1 tissues. In G. hirsutum, 151 non-repeated genes of the DREB and ERF subfamily genes were responsive to different stresses: 132 genes were induced by cold, 63 genes by drought and 94 genes by heat. qRT-PCR confirmed that 13 GhDREB and 15 GhERF genes were induced by cold and/or drought. No transcripts detected for 53 of the 111 tandem duplicated genes in TM-1. In addition, some homoeologous genes showed biased expression toward either A-or D-subgenome.

Conclusions

The AP2/EREBP genes were obviously expanded in Gossypium. The GhDREB and GhERF genes play crucial roles in cotton stress responses. Our genome-wide analysis of AP2/EREBP genes in cotton provides valuable information for characterizing the molecular functions of AP2/EREBP genes and reveals insights into their evolution in polyploid plants.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3517-9) contains supplementary material, which is available to authorized users.

Ectopic expression of a cytochrome P450 monooxygenase gene PtCYP714A3 from Populus trichocarpa reduces shoot growth and improves tolerance to salt stress in transgenic rice

In Arabidopsis thaliana and Oryza sativa, the cytochrome P450 (CYP) 714 protein family represents a unique group of CYP monooxygenase, which functions as a shoot-specific regulator in plant development through gibberellin deactivation. Here, we report the functional characterizations of PtCYP714A3, an OsCYP714D1/Eui homologue from Populus trichocarpa. PtCYP714A3 was ubiquitously expressed with the highest transcript level in cambium-phloem tissues, and was greatly induced by salt and osmotic stress in poplar. Subcellular localization analyses indicated that PtCYP714A3-YFP fusion protein was targeted to endoplasmic reticulum (ER). Expression of PtCYP714A3 in the rice eui mutant could rescue its excessive-shoot-growth phenotype. Ectopic expression of PtCYP714A3 in rice led to semi-dwarfed phenotype with promoted tillering and reduced seed size. Transgenic lines which showed significant expression of PtCYP714A3 also accumulated lower GA level than did the wild-type (WT) plants. The expression of some GA biosynthesis genes was significantly suppressed in these transgenic plants. Furthermore, transgenic rice plants exhibited enhanced tolerance to salt and maintained more Na(+) in both shoot and root tissues under salinity stress. All these results not only suggest a crucial role of PtCYP714A3 in shoot responses to salt toxicity in rice, but also provide a molecular basis for genetic engineering of salt-tolerant crops.

Nitric Oxide Mediated Transcriptome Profiling Reveals Activation of Multiple Regulatory Pathways in Arabidopsis thaliana

Imbalance between the accumulation and removal of nitric oxide and its derivatives is a challenge faced by all plants at the cellular level, and is especially important under stress conditions. Exposure of plants to various biotic and abiotic stresses causes rapid changes in cellular redox tone potentiated by the rise in reactive nitrogen species that serve as signaling molecules in mediating defensive responses. To understand mechanisms mediated by these signaling molecules, we performed a large-scale analysis of the Arabidopsis transcriptome induced by nitrosative stress. We generated an average of 84 and 91 million reads from three replicates each of control and 1 mM S-nitrosocysteine (CysNO)-infiltrated Arabidopsis leaf samples, respectively. After alignment, more than 95% of all reads successfully mapped to the reference and 32,535 genes and 55,682 transcripts were obtained. CysNO infiltration caused differential expression of 6436 genes (3448 up-regulated and 2988 down-regulated) and 6214 transcripts (3335 up-regulated and 2879 down-regulated) 6 h post-infiltration. These differentially expressed genes were found to be involved in key physiological processes, including plant defense against various biotic and abiotic stresses, hormone signaling, and other developmental processes. After quantile normalization of the FPKM values followed by student's T-test (P < 0.05) we identified 1165 DEGs (463 up-regulated and 702 down-regulated) with at least 2-folds change in expression after CysNO treatment. Expression patterns of selected genes involved in various biological pathways were verified using quantitative real-time PCR. This study provides comprehensive information about plant responses to nitrosative stress at transcript level and would prove helpful in understanding and incorporating mechanisms associated with nitrosative stress responses in plants.

Global changes in gene expression, assayed by microarray hybridization and quantitative RT-PCR, during acclimation of three Arabidopsis thaliana accessions to sub-zero temperatures after cold acclimation

During cold acclimation plants increase in freezing tolerance in response to low non-freezing temperatures. This is accompanied by many physiological, biochemical and molecular changes that have been extensively investigated. In addition, plants of many species, including Arabidopsis thaliana, become more freezing tolerant during exposure to mild, non-damaging sub-zero temperatures after cold acclimation. There is hardly any information available about the molecular basis of this adaptation. Here, we have used microarrays and a qRT-PCR primer platform covering 1,880 genes encoding transcription factors (TFs) to monitor changes in gene expression in the Arabidopsis accessions Columbia-0, Rschew and Tenela during the first 3 days of sub-zero acclimation at -3 °C. The results indicate that gene expression during sub-zero acclimation follows a tighly controlled time-course. Especially AP2/EREBP and WRKY TFs may be important regulators of sub-zero acclimation, although the CBF signal transduction pathway seems to be less important during sub-zero than during cold acclimation. Globally, we estimate that approximately 5% of all Arabidopsis genes are regulated during sub-zero acclimation. Particularly photosynthesis-related genes are down-regulated and genes belonging to the functional classes of cell wall biosynthesis, hormone metabolism and RNA regulation of transcription are up-regulated. Collectively, these data provide the first global analysis of gene expression during sub-zero acclimation and allow the identification of candidate genes for forward and reverse genetic studies into the molecular mechanisms of sub-zero acclimation.

A transcriptomic analysis of Chrysanthemum nankingense provides insights into the basis of low temperature tolerance

BACKGROUND

A major constraint affecting the quality and productivity of chrysanthemum is the unusual period of low temperature occurring during early spring, late autumn, and winter. Yet, there has been no systematic investigation on the genes underlying the response to low temperature in chrysanthemum. Herein, we used RNA-Seq platform to characterize the transcriptomic response to low temperature by comparing different transcriptome of Chrysanthemum nankingense plants and subjecting them to a period of sub-zero temperature, with or without a prior low temperature acclimation.

RESULTS

Six separate RNA-Seq libraries were generated from the RNA samples of leaves and stems from six different temperature treatments, including one cold acclimation (CA), two freezing treatments without prior CA, two freezing treatments with prior CA and the control. At least seven million clean reads were obtained from each library. Over 77% of the reads could be mapped to sets of C. nankingense unigenes established previously. The differentially transcribed genes (DTGs) were identified as low temperature sensing and signalling genes, transcription factors, functional proteins associated with the abiotic response, and low temperature-responsive genes involved in post-transcriptional regulation. The differential transcription of 15 DTGs was validated using quantitative RT-PCR.

CONCLUSIONS

The large number of DTGs identified in this study, confirmed the complexity of the regulatory machinery involved in the processes of low temperature acclimation and low temperature/freezing tolerance.

Functional characterization of an abiotic stress-inducible transcription factor AtERF53 in Arabidopsis thaliana

AP2/ERF proteins play crucial roles in plant growth and development and in responses to biotic and abiotic stresses. ETHYLENE RESPONSE FACTOR 53 (AtERF53) belongs to group 1 in the ERF family and is induced in the early hours of dehydration and salt treatment. The functional study of AtERF53 is hampered because its protein expression in Arabidopsis is vulnerable to degradation in overexpressed transgenic lines. Taking advantage of the RING domain ligase1/RING domain ligase2 (rglg1rglg2) double mutant in which the AtERF53 can express stably, we investigate the physiological function of AtERF53. In this study, we demonstrate that expression of AtERF53 in wild-type Arabidopsis was responsive to heat and abscisic acid (ABA) treatment. From results of the cotransfection experiment, we concluded that AtERF53 has positive transactivation activity. Overexpression of AtERF53 in the rglg1rglg2 double mutant conferred better heat-stress tolerance and had resulted in higher endogenous ABA and proline levels compared to rglg1rglg2 double mutants. AtERF53 also has a function to regulate guard-cell movement because the stomatal aperture of AtERF53 overexpressed in rglg1rglg2 double mutant was smaller than that in the rglg1rglg2 double mutant under ABA treatment. In a global gene expression study, we found higher expressions of many stress-related genes, such as DREB1A, COR15A, COR15B, PLC, P5CS1, cpHSC70 s and proline and ABA metabolic-related genes. Furthermore, we identified several downstream target genes of AtERF53 by chromatin immunoprecipitation assay. In conclusion, the genetic, molecular and biochemical result might explain how AtERF53 serving as a transcription factor contributes to abiotic stress tolerance in Arabidopsis.

Isolation and functional characterization of a salt responsive transcriptional factor, LrbZIP from lotus root (Nelumbo nucifera Gaertn)

Basic leucine zipper transcription factor (bZIP) is involved in signaling transduction for various stress responses. Here we reported a bZIP transcription factor (accession: JX887153) isolated from a salt-resistant lotus root using cDNA-AFLP approach with RT-PCR and RACE-PCR method. Full-length cDNA which consisted of a single open reading frame encoded a putative polypeptide of 488 amino acids. On the basis of 78, 76, and 75 % sequence similarity with the bZIPs from Medicago truncatula (XP_003596814.1), Carica papaya (ABS01351.1) and Arabidopsis thaliana (NP_563810.2), we designed it as LrbZIP. Semi quantitative RT-PCR results, performed on the total RNA extracted from tips of lotus root, showed that LrbZIP expression was increased with 250 mM NaCl treatment for 18 h. Effects of low temperature on the expression of LrbZIP was also studied, and its expression was significantly enhanced with a 4 °C treatment for 12 h. In addition, LrbZIP expression was strongly induced by treatment with exogenous 100 μM ABA. To evaluate its function across the species, tobacco (Nicotiana tabacum L.) was transformed with LrbZIP in a binary vector construct. Transgenic plants exhibited higher resistance as compared with the control according to the results of the root growth, chlorophyll content and electrolyte leakage when exposed to NaCl treatment. In addition, LrCDPK2, LrLEA, and TPP also showed enhanced expression in the transgenic plants. Overall, expression of LrbZIP was probably very important for salt-resistant lotus root to survive through salt stress.

An active ac/ds transposon system for activation tagging in tomato cultivar m82 using clonal propagation

Tomato (Solanum lycopersicum) is a model organism for Solanaceae in both molecular and agronomic research. This project utilized Agrobacterium tumefaciens transformation and the transposon-tagging construct Activator (Ac)/Dissociator (Ds)-ATag-Bar_gosGFP to produce activation-tagged and knockout mutants in the processing tomato cultivar M82. The construct carried hygromycin resistance (hyg), green fluorescent protein (GFP), and the transposase (TPase) of maize (Zea mays) Activator major transcript X054214.1 on the stable Ac element, along with a 35S enhancer tetramer and glufosinate herbicide resistance (BAR) on the mobile Ds-ATag element. An in vitro propagation strategy was used to produce a population of 25 T0 plants from a single transformed plant regenerated in tissue culture. A T1 population of 11,000 selfed and cv M82 backcrossed progeny was produced from the functional T0 line. This population was screened using glufosinate herbicide, hygromycin leaf painting, and multiplex polymerase chain reaction (PCR). Insertion sites of transposed Ds-ATag elements were identified through thermal asymmetric interlaced PCR, and resulting product sequences were aligned to the recently published tomato genome. A population of 509 independent, Ds-only transposant lines spanning all 12 tomato chromosomes has been developed. Insertion site analysis demonstrated that more than 80% of these lines harbored Ds insertions conducive to activation tagging. The capacity of the Ds-ATag element to alter transcription was verified by quantitative real-time reverse transcription-PCR in two mutant lines. The transposon-tagged lines have been immortalized in seed stocks and can be accessed through an online database, providing a unique resource for tomato breeding and analysis of gene function in the background of a commercial tomato cultivar.

Generating high temperature tolerant transgenic plants: Achievements and challenges

Production of plants tolerant to high temperature stress is of immense significance in the light of global warming and climate change. Plant cells respond to high temperature stress by re-programming their genetic machinery for survival and reproduction. High temperature tolerance in transgenic plants has largely been achieved either by over-expressing heat shock protein genes or by altering levels of heat shock factors that regulate expression of heat shock and non-heat shock genes. Apart from heat shock factors, over-expression of other trans-acting factors like DREB2A, bZIP28 and WRKY proteins has proven useful in imparting high temperature tolerance. Besides these, elevating the genetic levels of proteins involved in osmotic adjustment, reactive oxygen species removal, saturation of membrane-associated lipids, photosynthetic reactions, production of polyamines and protein biosynthesis process have yielded positive results in equipping transgenic plants with high temperature tolerance. Cyclic nucleotide gated calcium channel proteins that regulate calcium influxes across the cell membrane have recently been shown to be the key players in induction of high temperature tolerance. The involvement of calmodulins and kinases in activation of heat shock factors has been implicated as an important event in governing high temperature tolerance. Unfilled gaps limiting the production of high temperature tolerant transgenic plants for field level cultivation are discussed.

Identification of wild soybean (Glycine soja) TIFY family genes and their expression profiling analysis under bicarbonate stress

Wild soybean (Glycine soja L. G07256) exhibits a greater adaptability to soil bicarbonate stress than cultivated soybean, and recent discoveries show that TIFY family genes are involved in the response to several abiotic stresses. A genomic and transcriptomic analysis of all TIFY genes in G. soja, compared with G. max, will provide insight into the function of this gene family in plant bicarbonate stress response. This article identified and characterized 34 TIFY genes in G. soja. Sequence analyses indicated that most GsTIFY proteins had two conserved domains: TIFY and Jas. Phylogenetic analyses suggested that these GsTIFY genes could be classified into two groups. A clustering analysis of all GsTIFY transcript expression profiles from bicarbonate stress treated G. soja showed that there were five different transcript patterns in leaves and six different transcript patterns in roots when the GsTIFY family responds to bicarbonate stress. Moreover, the expression level changes of all TIFY genes in cultivated soybean, treated with bicarbonate stress, were also verified. The expression comparison analysis of TIFYs between wild and cultivated soybeans confirmed that, different from the cultivated soybean, GsTIFY (10a, 10b, 10c, 10d, 10e, 10f, 11a, and 11b) were dramatically up-regulated at the early stage of stress, while GsTIFY 1c and 2b were significantly up-regulated at the later period of stress. The frequently stress responsive and diverse expression profiles of the GsTIFY gene family suggests that this family may play important roles in plant environmental stress responses and adaptation.

STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in Arabidopsis and rice

Understanding the principles of abiotic and biotic stress responses, tolerance and adaptation remains important in plant physiology research to develop better varieties of crop plants. Better understanding of plant stress response mechanisms and application of knowledge derived from integrated experimental and bioinformatics approaches are gaining importance. Earlier, we showed that compiling a database of stress-responsive transcription factors and their corresponding target binding sites in the form of Hidden Markov models at promoter, untranslated and upstream regions of stress-up-regulated genes from expression analysis can help in elucidating various aspects of the stress response in Arabidopsis. In addition to the extensive content in the first version, STIFDB2 is now updated with 15 stress signals, 31 transcription factors and 5,984 stress-responsive genes from three species (Arabidopsis thaliana, Oryza sativa subsp. japonica and Oryza sativa subsp. indica). We have employed an integrated biocuration and genomic data mining approach to characterize the data set of transcription factors and consensus binding sites from literature mining and stress-responsive genes from the Gene Expression Omnibus. STIFDB2 currently has 38,798 associations of stress signals, stress-responsive genes and transcription factor binding sites predicted using the Stress-responsive Transcription Factor (STIF) algorithm, along with various functional annotation data. As a unique plant stress regulatory genomics data platform, STIFDB2 can be utilized for targeted as well as high-throughput experimental and computational studies to unravel principles of the stress regulome in dicots and gramineae. STIFDB2 is available from the URL: http://caps.ncbs.res.in/stifdb2.