TGACG-BINDING FACTORs (TGAs) and TGA-interacting CC-type glutaredoxins modulate hyponastic growth in Arabidopsis thaliana

Redox-inactive CC-type glutaredoxins interfere with TGA transcription factor-dependent repression of target promoters in roots

Changes in nitrogen (N) availability in the soil trigger transcriptional responses in plants to optimize N acquisition, allocation, and remobilization. In roots of N-starved Arabidopsis (Arabidopsis thaliana) plants, transcriptional activation of genes encoding, for example, low-affinity nitrate transporters, depends on 4 related C-TERMINALLY ENCODED PEPTIDE DOWNSTREAM (CEPD) proteins, also known as ROXY6, ROXY7, ROXY8, and ROXY9. All 21 ROXYs found in A. thaliana interact with members of the TGACG-binding (TGA) family of transcription factors. Here, we demonstrate that 2 Clade I TGAs (TGA1, TGA4) serve as molecular links between CEPDs and their target promoters in roots. In the roxy6 roxy7 roxy8 roxy9 quadruple mutant (named cepd in this manuscript), transcriptional activation of N-starvation-inducible genes is impaired, most likely due to the association of Clade I TGAs with a repressive complex at their target promoters. In wild-type plants, this repressive complex is nonfunctional, and gene expression may be regulated by the N supply-regulated ratio of CEPDs over opposing ROXYs containing the TOPLESS-interacting ALWL motif. Although CEPDs resemble glutaredoxins with glutathione-dependent oxidoreductase activity, a ROXY9 variant with a mutation in the catalytic cysteine in its putative active site can confer wild-type-like regulation of target genes. This finding demonstrates that ROXY9 does not function through redox-dependent mechanisms.

CmTGA8-CmAPX1/CmGSTU25 regulatory model involved in trehalose induced cold tolerance in oriental melon seedlings

Plants have developed complex regulatory networks to adapt to various stresses, including cold stress. Trehalose (Tre), known as the "sugar of life," plays a crucial role in enhancing cold tolerance by triggering antioxidation. However, the underlying regulatory mechanisms remain unclear. This study examines the transcription factor gene CmTGA8, which is induced by Tre under normal and cold conditions in melon seedlings (Cucumis melo L.), through transcriptome analysis and RT-qPCR. Reverse genetic analyses showed that silencing CmTGA8 reduced ascorbate peroxidase (APX) and glutathione S-transferase (GST) activities, suppressed CmAPX1 and CmGSTU25 expression, and increased cold susceptibility in melon seedlings. Our previous reports illustrated that Tre treatment significantly induced the expression of respiratory burst oxidase homologues (CmRBOHD) gene, encoding NADPH oxidases responsible for generating apoplastic H2O2. Silencing CmRBOHD markedly inhibited CmTGA8, CmAPX1, and CmGSTU25 expression and reduced cold tolerance. Moreover, H2O2 treatment upregulated CmTGA8 expression, while the NADPH oxidase inhibitor diphenyleneiodonium (DPI) treatment downregulated it. Additionally, CmTGA8 physically interacted with CmAPX1 and CmGSTU25 to promote their expression. Silencing CmGSTU25 decreased GST activity and ferric reducing ability of plasma (FRAP), further increasing cold sensitivity. These findings identify a novel regulatory hierarchy of the H2O2-CmTGA8-CmAPX1/CmGSTU25 cascade in the Tre-mediated cold response pathway in melon seedlings.

Regulation of PILS genes by bZIP transcription factor TGA7 in tomato plant growth

Auxin plays a pivotal role in plant growth regulation. The PIN-FORMED (PIN) proteins facilitate long-distance polar auxin transport, whereas the recently identified PIN-LIKES (PILS) proteins regulate intracellular auxin homeostasis. However, the auxin transport mechanisms in horticultural crops remain largely unexplored. Here, we identified and characterized PILS genes in tomato (Solanum lycopersicum). Promoter analysis revealed enrichment in TGA[C/T]G motifs, suggesting transcriptional regulation by TGA factors in the bZIP family. Subcellular localization studies confirmed that all tomato PILS proteins localize in the endoplasmic reticulum. PILS2 exhibited the highest expression across examined tissues, and its close homologue PILS6 showed a similar but less pronounced expression pattern. Silencing PILS2 significantly inhibited shoot and root growth. Phylogenetic and expression analyses identified the homologs of Arabidopsis TGA1, TGA3, TGA4, and TGA7 in tomato genome, with tomato TGA7 showing higher expression in roots. Notably, silencing tomato TGA7, but not TGA1, TGA3, or TGA4, strongly impaired shoot and root growth. Molecular assays demonstrated that TGA7 directly binds to the PILS2 promoter to activate its transcription. These findings uncover a TGA7-PILS2 regulatory module that governs plant growth and offer new insights into the function and regulation of PILS genes in tomato.

Genome-Wide Identification and Expression Analysis of the TGA Gene Family in Banana (Musa nana Lour.) Under Various Nitrogen Conditions

The TGA (TGACG motif-binding factor) transcription factors are integral to root growth and development, and are pivotal in mediating plant responses to abiotic stresses. Nonetheless, their role in the nutrient absorption processes of banana plants has not been extensively investigated. This research conducted a comprehensive analysis of the MaTGA gene family, emphasizing their physicochemical characteristics, phylogenetic relationships, gene duplication events, promoter cis-regulatory elements and protein interaction networks. Furthermore, this study investigated the expression patterns of MaTGA family members under varying nitrogen conditions. A total of 18 MaTGA members were identified within the banana genome, each encoding proteins characterized by the presence of bZIP and DOG domains. These genes exhibited an uneven distribution across eight chromosomes. Phylogenetic analysis further classified the MaTGA family into four distinct subgroups (I-IV), consisting of three, seven, three, and five members, respectively. An analysis of promoter cis-elements indicated that over 50% of the MaTGA gene family members contain hormone-responsive elements associated with abscisic acid (ABRE), ethylene (ERE), and salicylic acid (SARE), in addition to stress-responsive elements related to drought (MBS) and low temperature (LTR). Regarding gene expression, MaTGA7, MaTGA8, and MaTGA15 exhibited significantly elevated expression levels in the leaves and roots relative to other tissues. Under varying nitrogen conditions, 13 members, including MaTGA7 and MaTGA8, demonstrated the highest expression levels under reduced nitrogen (70%) treatment, followed by low nitrogen (20%) conditions, and the lowest expression levels were observed under nitrogen-deficient conditions. These findings imply that MaTGA genes may play crucial roles in enhancing nitrogen use efficiency. Protein interaction predictions suggest that MaTGA7, MaTGA8, and MaTGA15 may interact with nitrogen-related proteins, including Nitrate Transporter 2 (NRT2.1 and NRT2.2), NIN-Like Protein 7 (NLP7), and Nitrate Transporter 1.1 (NPF6.3). In summary, MaTGA7, MaTGA8, and MaTGA15 are likely involved in the processes of nitrogen absorption and utilization in bananas. The present findings establish a basis for subsequent investigations into the functional roles of MaTGA genes in augmenting nutrient use efficiency and mediating responses to abiotic stresses in banana plants.

Transcriptomic analysis reveals the crucial role of YABBY genes family in hormonal induced parthenocarpy in Cucumis sativus L

BACKGROUND

The plant-specific YABBY transcription factor family plays several activities, including responding to abiotic stress, establishing dorsoventral polarity, and developing lateral organs. Cucumis sativus L. commonly referred to as cucumber and one of the first vegetable crops with a fully sequenced genome.

RESULTS

In this work, we examined the application of NAA, CPPU, and GA4 + 7 to inflict parthenocarpy in the cucumber ZK line. The expression pattern of YABBY genes throughout fruit development and performed a genomic census of cucumber (Cucumis sativus L.). Based on peptide classification, we discovered eight CsYABBY genes and divided them into five subfamilies. Similarities in motif composition and exon-intron structure were also observed. The cis-elements and gene ontology (GO) analysis revealed the involvement of CsYABBY genes in vegetative growth and the transition of vegetative to the reproductive phase. The expression analysis revealed the differential expression response to NAA, CPPU, and GA4 + 7. In particular, the CsYABBY1 was induced sharply by NAA and CPPU but not GA4 + 7. The transient expression of CsCRC disclosed that it is localized in the nucleus.

CONCLUSION

These findings point to the possibility that CsYABBY1 and CsCRC may positively affect fruit development and could be utilized to generate parthenocarpic cucumber fruits.

Molecular basis for the enzymatic inactivity of class III glutaredoxin ROXY9 on standard glutathionylated substrates

Class I glutaredoxins (GRXs) are nearly ubiquitous proteins that catalyse the glutathione (GSH)-dependent reduction of mainly glutathionylated substrates. In land plants, a third class of GRXs has evolved (class III). Class III GRXs regulate the activity of TGA transcription factors through yet unexplored mechanisms. Here we show that Arabidopsis thaliana class III GRX ROXY9 is inactive as an oxidoreductase on widely used model substrates. Glutathionylation of the active site cysteine, a prerequisite for enzymatic activity, occurs only under highly oxidizing conditions established by the GSH/glutathione disulfide (GSSG) redox couple, while class I GRXs are readily glutathionylated even at very negative GSH/GSSG redox potentials. Thus, structural alterations in the GSH binding site leading to an altered GSH binding mode likely explain the enzymatic inactivity of ROXY9. This might have evolved to avoid overlapping functions with class I GRXs and raises questions of whether ROXY9 regulates TGA substrates through redox regulation.

PP2 gene family in Phyllostachys edulis: identification, characterization, and expression profiles

BACKGROUND

Phloem protein 2 (PP2), a dimeric lectin, is known for its involvement in plant responses to biotic and abiotic stresses. However, research on PP2 proteins in Moso bamboo is lacking.

RESULTS

In this study, comprehensive genome-wide analysis of the PP2-like gene family was conducted in Moso bamboo (Phyllostachys edulis), which has a significant economic and ecological value. Using HMMER3 search and InterPro domain analysis, 23 PP2-like genes (PhePP2-1 to PhePP2-23) were identified in the P. edulis genome. These genes were distributed across 12 chromosomal scaffolds, with proteins ranging from 216 to 556 amino acids in length. Phylogenetic analysis, including 163 PP2 proteins from eight plant species, revealed six distinct groups, with Group III and Group V being the largest. Gene structure and motif analyses indicated conserved domains across the PhePP2 proteins. In addition, Cis-element analysis of the promoter regions highlighted their potential regulatory roles in hormone, stress, and light responses. Expression pattern analysis using RNA-seq data showed differential expression of PhePP2 genes under drought, salt, salicylic acid, and abscisic acid treatments, indicating their involvement in stress response pathways. Furthermore, qPCR validation in different tissues and organs of Moso bamboo confirmed the expression profiles of the selected PhePP2 genes.

CONCLUSIONS

This study provides a comprehensive understanding of the functional roles of PP2-like genes in Moso bamboo and insights into their potential applications in enhancing stress tolerance and growth in plants.

A CC-Type Glutaredoxins GRX480 Functions in Cadmium Tolerance by Maintaining Redox Homeostasis in Arabidopsis

Cadmium (Cd) toxicity causes oxidative stress damage in plant cells. Glutaredoxins (GRXs), a type of small oxidoreductase, play a crucial role in modulating thiol redox states. However, whether GRXs act in Cd stress remains to be identified. Here, we reveal that Arabidopsis GRX480, a member of the CC-type family, enhances plant Cd stress tolerance. The GRX480 mutants exhibit enhanced sensitivity to Cd stress, manifested by shortened root, reduced biomass, lower chlorophyll and proline levels, and decreased photosynthetic efficiency compared with the wild type. The Cd concentration in GRX480 mutants is higher than the wild type, resulting from the inhibition of Cd efflux and transport genes transcription. Lower levels of GSH were detected in Cd-treated GRX480 mutants than in the wild type, indicating that GRX480 regulates plant Cd tolerance by influencing the balance between GSH and GSSG. Furthermore, the hyperaccumulation of reactive oxygen species (ROS) is associated with decreased expression of H2O2 scavenging genes in Cd-treated GRX480 mutants. Additionally, more toxic reactive carbonyl species (RCS), produced during oxidative stress, accumulate in Cd-treated GRX480 mutants than in wild type. Overall, our study establishes a critical role of GRX480 in response to Cd stress, highlighting its multifaceted contributions to detoxification and the maintenance of redox homeostasis.

The AP2/ERF transcription factor ORA59 regulates ethylene-induced phytoalexin synthesis through modulation of an acyltransferase gene expression

The gaseous ethylene (ET) and the oxylipin-derived jasmonic acid (JA) in plants jointly regulate an arsenal of pathogen responsive genes involved in defending against necrotrophic pathogens. The APETALA2 (AP2)/ETHYLENE RESPONSE FACTOR (ERF) transcription factor ORA59 is a major positive regulator of the ET/JA-mediated defense pathway in Arabidopsis thaliana. The Arabidopsis agmatine coumaroyltransferase (AtACT) catalyzes the formation of hydroxycinnamic acid amides (HCAAs) which are effective toxic antimicrobial substances known as phytoalexins and play an important role in plant defense response. However, induction and regulation of AtACT gene expression and HCAAs synthesis in plants remain less understood. Through gene coexpression network analysis, we identified a list of GCC-box cis-element containing genes that were coexpressed with ORA59 under diverse biotic stress conditions and might be potential downstream targets of this AP2/ERF-domain transcription factor. Particularly, ORA59 directly binds to AtACT gene promoter via the GCC-boxes and activates AtACT gene expression. The ET precursor 1-aminocyclopropane-1-carboxylic acid (ACC)-treatment significantly induces AtACT gene expression. Both ORA59 and members of the class II TGA transcription factors are indispensable for ACC-induced AtACT expression. Interestingly, the expression of AtACT is also subject to the signaling crosstalk of the salicylic acid- and ET/JA-mediated defense response pathways. In addition, we found that genes of the phenylpropanoid metabolism pathway were specifically induced by Botrytis cinerea. Taking together, these evidence suggest that the ET/JA signaling pathway activate the expression of AtACT to increase antimicrobial HCAAs production through the transcription factor ORA59 in response to the infection of necrotrophic plant pathogens.

Integration of shoot-derived polypeptide signals by root TGA transcription factors is essential for survival under fluctuating nitrogen environments

Unlike plants in the field, which experience significant temporal fluctuations in environmental conditions, plants in the laboratory are typically grown in controlled, stable environments. Therefore, signaling pathways evolved for survival in fluctuating environments often remain functionally latent in laboratory settings. Here, we show that TGA1 and TGA4 act as hub transcription factors through which the expression of genes involved in high-affinity nitrate uptake are regulated in response to shoot-derived phloem mobile polypeptides, CEP DOWNSTREAM 1 (CEPD1), CEPD2 and CEPD-like 2 (CEPDL2) as nitrogen (N) deficiency signals, and Glutaredoxin S1 (GrxS1) to GrxS8 as N sufficiency signals. CEPD1/2/CEPDL2 and GrxS1-S8 competitively bind to TGA1/4 in roots, with the former acting as transcription coactivators that enhance the uptake of nitrate, while the latter function as corepressor complexes together with TOPLESS (TPL), TPL-related 1 (TPR1) and TPR4 to limit nitrate uptake. Arabidopsis plants deficient in TGA1/4 maintain basal nitrate uptake and exhibit growth similar to wild-type plants in a stable N environment, but are impaired in regulation of nitrate acquisition in response to shoot N demand, leading to defective growth under fluctuating N environments where rhizosphere nitrate ions switch periodically between deficient and sufficient states. TGA1/4 are crucial transcription factors that enable plants to survive under fluctuating and challenging N environmental conditions.

An evolutionary view of the function of CC-type glutaredoxins in plant development and adaptation to the environment

Land plants have to face an oxidizing, heterogeneous, and fast changing environment. Redox-dependent post-translational modifications emerge as a critical component of plant responses to stresses. Among the thiol oxidoreductase superfamily, class III CC-type glutaredoxins (called ROXYs) are land plant specific, and their evolutionary history is highly dynamic. Angiosperms encode many isoforms, classified into five subgroups (Aα, Aβ, Bα, Bβ, Bγ) that probably evolved from five common ancestral ROXYs, with higher evolutionary dynamics in the Bγ subgroup compared with the other subgroups. ROXYs can modulate the transcriptional activity of TGA transcription factor target genes, although their biochemical function is still debated. ROXYs participate in the control of proper plant development and reproduction, and are mainly negative regulators of plant responses to biotic and abiotic stresses. This suggests that most ROXYs could play essential and conserved functions in resetting redox-dependent changes in transcriptional activity upon stress signaling to ensure the responsiveness of the system and/or avoid exaggerated responses that could lead to major defects in plant growth and reproduction. In Arabidopsis Bγ members acquired important functions in responses to nitrogen availability and endogenous status, but the rapid and independent evolution of this subclass might suggest that this function results from neofunctionalization, specifically observed in core eudicots.

Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin in Arabidopsis thaliana L

In plant hormone signaling, transcription factor regulatory networks (TFRNs), which link the master transcription factors to the biological processes under their control, remain insufficiently characterized despite their crucial function. Here, we identify a TFRN involved in the response to the key plant hormone auxin and define its impact on auxin-driven biological processes. To reconstruct the TFRN, we developed a three-step procedure, which is based on the integrated analysis of differentially expressed gene lists and a representative collection of transcription factor binding profiles. Its implementation is available as a part of the CisCross web server. With the new method, we distinguished two transcription factor subnetworks. The first operates before auxin treatment and is switched off upon hormone application, the second is switched on by the hormone. Moreover, we characterized the functioning of the auxin-regulated TFRN in control of chlorophyll and lignin biosynthesis, abscisic acid signaling, and ribosome biogenesis.

Capsicum chinense Jacq.-derived glutaredoxin (CcGRXS12) alters redox status of the cells to confer resistance against pepper mild mottle virus (PMMoV-I)

KEY MESSAGE

The CcGRXS12 gene protects plants from cellular oxidative damage that are caused by both biotic and abiotic stresses. The protein possesses GSH-disulphide oxidoreductase property but lacks Fe-S cluster assembly mechanism. Glutaredoxins (Grxs) are small, ubiquitous and multi-functional proteins. They are present in different compartments of plant cells. A chloroplast targeted Class I GRX (CcGRXS12) gene was isolated from Capsicum chinense during the pepper mild mottle virus (PMMoV) infection. Functional characterization of the gene was performed in Nicotiana benthamiana transgenic plants transformed with native C. chinense GRX (Nb:GRX), GRX-fused with GFP (Nb:GRX-GFP) and GRX-truncated for chloroplast sequences fused with GFP (Nb:Δ2MGRX-GFP). Overexpression of CcGRXS12 inhibited the PMMoV-I accumulation at the later stage of infection, accompanied with the activation of salicylic acid (SA) pathway pathogenesis-related (PR) transcripts and suppression of JA/ET pathway transcripts. Further, the reduced accumulation of auxin-induced Glutathione-S-Transferase (pCNT103) in CcGRXS12 overexpressing lines indicated that the protein could protect the plants from the oxidative stress caused by the virus. PMMoV-I infection increased the accumulation of pyridine nucleotides (PNs) mainly due to the reduced form of PNs (NAD(P)H), and it was high in Nb:GRX-GFP lines compared to other transgenic lines. Apart from biotic stress, CcGRXS12 protects the plants from abiotic stress conditions caused by H2O2 and herbicide paraquat. CcGRXS12 exhibited GSH-disulphide oxidoreductase activity in vitro; however, it was devoid of complementary Fe-S cluster assembly mechanism found in yeast. Overall, this study proves that CcGRXS12 plays a crucial role during biotic and abiotic stress in plants.

Molecular identification and functional characterization of an environmental stress responsive glutaredoxin gene ROXY1 in Quercus glauca

Quercus glauca is a valuable natural resource with both economic and ecological values. It is one of the dominant forest tree species widely distributed in Southern China. As a perennial broadleaf plant, Q. glauca inevitably encounters numerous stresses from environment. Glutaredoxins (GRXs) are a kind of small oxidoreductases that play an important role in response to oxidative stress. CC-type GRXs also known as ROXYs are specific to land plants. In this study, we isolated a CC-type GRX gene, QgROXY1, from Q. glauca. Expression of QgROXY1 is induced by a variety of environmental stimuli. QgROXY1 protein localizes to both cytoplasm and nucleus; whereas the nucleus localized QgROXY1 could physically interact with the basic region/leucine zipper motif (bZIP) transcription factor AtTGA2 from Arabidopsis thaliana. Transgenic A. thaliana ectopically expressing QgROXY1 is hypersensitive to exogenously applied salicylic acid. Induction of plant defense gene is significantly impaired in QgROXY1 transgenic plants that results in enhanced susceptibility to infection of Botrytis cinerea pathogen, indicating the evolutionary conserved function among ROXY homologs in weedy and woody plants. This is the first described function for the ROXYs in tree plants. Through this case study, we demonstrated the feasibility and efficacy of molecular technology applied to characterization of gene function in tree species.

Functional characterization of GhNAC2 promoter conferring hormone- and stress-induced expression: a potential tool to improve growth and stress tolerance in cotton

The GhNAC2 transcription factor identified from G. herbaceum improves root growth and drought tolerance through transcriptional reprogramming of phytohormone signaling. The promoter of such a versatile gene could serve as an important genetic engineering tool for biotechnological application. In this study, we identified and characterized the promoter of GhNAC2 to understand its regulatory mechanism. GhNAC2 transcription factor increased in root tissues in response to GA, ethylene, auxin, ABA, mannitol, and NaCl. In silico analysis revealed an overrepresentation of cis-regulatory elements associated with hormone signaling, stress responses and root-, pollen-, and seed-specific promoter activity. To validate their role in GhNAC2 function/regulation, an 870-bp upstream regulatory sequence was fused with the GUS reporter gene (uidA) and expressed in Arabidopsis and cotton hairy roots for in planta characterization. Histochemical GUS staining indicated localized expression in root tips, root elongation zone, root primordia, and reproductive tissues under optimal growth conditions. Mannitol, NaCl, auxin, GA, and ABA, induced the promoter-driven GUS expression in all tissues while ethylene suppressed the promoter activity. The results show that the 870 nt fragment of the GhNAC2 promoter drives root-preferential expression and responds to phytohormonal and stress signals. In corroboration with promoter regulation, GA and ethylene pathways differentially regulated root growth in GhNAC2-expressing Arabidopsis. The findings suggest that differential promoter activity governs the expression of GhNAC2 in root growth and stress-related functions independently through specific promoter elements. This multifarious promoter can be utilized to develop yield and climate resilience in cotton by expanding the options to control gene regulation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01411-2.

HISTONE DEACETYLASE 6 interaction with ABSCISIC ACID-INSENSITIVE 5 decreases apple drought tolerance

Understanding the molecular regulation of plant response to drought is the basis of drought-resistance improvement through molecular strategies. Here, we characterized apple (Malus × domestica) histone deacetylase 6 (MdHDA6), which negatively regulates apple drought tolerance by catalyzing deacetylation on histones associated with drought-responsive genes. Transgenic apple plants over-expressing MdHDA6 were less drought-tolerant, while those with down-regulated MdHDA6 expression were more drought-resistant than nontransgenic apple plants. Transcriptomic and histone 3 acetylation (H3ac) Chromatin immunoprecipitation-seq analyses indicated that MdHDA6 could facilitate histone deacetylation on the drought-responsive genes, repressing gene expression. Moreover, MdHDA6 interacted with the abscisic acid (ABA) signaling transcriptional factor, ABSCISIC ACID-INSENSITIVE 5 (MdABI5), forming the MdHDA6-MdABI5 complex. Interestingly, MdHDA6 facilitated histone deacetylation on the drought-responsive genes regulated by MdABI5, resulting in gene repression. Furthermore, a dual-Luc experiment showed that MdHDA6 could repress the regulation of a drought-responsive gene, RESPONSIVE TO DESICCATION 29A (MdRD29A) activated by MdABI5. On the one hand, MdHDA6 can facilitate histone deacetylation and gene repression on the positive drought-responsive genes to negatively regulate drought tolerance in apple. On the other hand, MdHDA6 directly interacts with MdABI5 and represses the expression of genes downstream of MdABI5 via histone deacetylation around these genes to reduce drought tolerance. Our study uncovers a different drought response regulatory mechanism in apple based on the MdHDA6-MdABI5 complex function and provides the molecular basis for drought-resistance improvement in apple.

Genome-wide analysis reveals regulatory mechanisms and expression patterns of TGA genes in peanut under abiotic stress and hormone treatments

INTRODUCTION

The TGA transcription factors, plays a crucial role in regulating gene expression. In cultivated peanut (Arachis hypogaea), which faces abiotic stress challenges, understanding the role of TGAs is important.

METHODS

In this study, we conducted a comprehensive in analysis of the TGA gene family in peanut to elucidate their regulatory mechanisms and expression patterns under abiotic stress and hormone treatments. Furthermore, functional studies on the representative AhTGA gene in peanut cultivars were conducted using transgenic Arabidopsis and soybean hair roots.

RESULTS

The genome-wide analysis revealed that a total of 20 AhTGA genes were identified and classified into five subfamilies. Collinearity analysis revealed that AhTGA genes lack tandem duplication, and their amplification in the cultivated peanut genome primarily relies on the whole-genome duplication of the diploid wild peanut to form tetraploid cultivated peanut, as well as segment duplication between the A and B subgenomes. Promoter and Protein-protein interaction analysis identified a wide range of cis-acting elements and potential interacting proteins associated with growth and development, hormones, and stress responses. Expression patterns of AhTGA genes in different tissues, under abiotic stress conditions for low temperature and drought, and in response to hormonal stimuli revealed that seven AhTGA genes from groups I (AhTGA04, AhTGA14 and AhTGA20) and II (AhTGA07, AhTGA11, AhTGA16 and AhTGA18) are involved in the response to abiotic stress and hormonal stimuli. The hormone treatment results indicate that these AhTGA genes primarily respond to the regulation of jasmonic acid and salicylic acid. Overexpressing AhTGA11 in Arabidopsis enhances resistance to cold and drought stress by increasing antioxidant activities and altering endogenous hormone levels, particularly ABA, SA and JA.

DISCUSSION

The AhTGA genes plays a crucial role in hormone regulation and stress response during peanut growth and development. The findings provide insights into peanut's abiotic stress tolerance mechanisms and pave the way for future functional studies.

Redox regulation, thioredoxins, and glutaredoxins in retrograde signalling and gene transcription

Integration of reactive oxygen species (ROS)-mediated signal transduction pathways via redox sensors and the thiol-dependent signalling network is of increasing interest in cell biology for their implications in plant growth and productivity. Redox regulation is an important point of control in protein structure, interactions, cellular location, and function, with thioredoxins (TRXs) and glutaredoxins (GRXs) being key players in the maintenance of cellular redox homeostasis. The crosstalk between second messengers, ROS, thiol redox signalling, and redox homeostasis-related genes controls almost every aspect of plant development and stress response. We review the emerging roles of TRXs and GRXs in redox-regulated processes interacting with other cell signalling systems such as organellar retrograde communication and gene expression, especially in plants during their development and under stressful environments. This approach will cast light on the specific role of these proteins as redox signalling components, and their importance in different developmental processes during abiotic stress.

Breakdown of Arabidopsis thaliana thioredoxins and glutaredoxins based on electrostatic similarity-Leads to common and unique interaction partners and functions

The reversible reduction and oxidation of protein thiols was first described as mechanism to control light/dark-dependent metabolic regulation in photosynthetic organisms. Today, it is recognized as an essential mechanism of regulation and signal transduction in all kingdoms of life. Proteins of the thioredoxin (Trx) family, Trxs and glutaredoxins (Grxs) in particular, catalyze thiol-disulfide exchange reactions and are vital players in the operation of thiol switches. Various Trx and Grx isoforms are present in all compartments of the cell. These proteins have a rather broad but at the same time distinct substrate specificity. Understanding the molecular basis of their target specificity is central to the understanding of physiological and pathological redox signaling. Electrostatic complementarity of the redoxins with their target proteins has been proposed as a major reason. Here, we analyzed the electrostatic similarity of all Arabidopsis thaliana Trxs, Grxs, and proteins containing such domains. Clustering of the redoxins based on this comparison suggests overlapping and also distant target specificities and thus functions of the different sub-classes including all Trx isoforms as well as the three classes of Grxs, i.e. CxxC-, CGFS-, and CC-type Grxs. Our analysis also provides a rationale for the tuned substrate specificities of both the ferredoxin- and NADPH-dependent Trx reductases.

Development of a protoplast isolation system for functional gene expression and characterization using petals of Camellia Oleifera

Protoplasts preparation and purification have been frequently used in plant genetics and breeding studies, whereas application of protoplasts in woody plants is still in its infancy. Although transient gene expression using purified protoplasts is well-documented and widely used in model plants and agriculture crops, no instance of either stable transformation or transient gene expression in the woody plant Camellia Oleifera has as of yet been reported. Here, we developed a protoplast preparation and purification method using C. oleifera petals by optimizing osmotic condition with D-mannitol and polysaccharide-degrading enzyme concentrations for petal cell wall digestion, to reach a high efficiency of protoplast productivity and viability. The achieved protoplasts yield was approximately 1.42 × 107 cells per gram of petal material and the viability of protoplasts was up to 89%. In addition, we explored influencing factors of protoplast transformation, including concentrations of PEG4000 and plasmid DNA. The transformation efficiency of 81% could be reached under the optimized condition. This protoplast isolation and transient expression system were deployed to further identify the functional regulation of C. oleifera related genes and the subcellular distribution of their encoded products. In summary, the protoplast isolation and transient expression system we established using oil-tea tree petals is an efficient, versatile and time-saving system, being suitable for gene function characterization and molecular mechanism analysis.

Exogenous application of salicylic acid improves freezing stress tolerance in alfalfa

Freezing stress is one of the most detrimental environmental factors that can seriously impact the growth, development, and distribution of alfalfa (Medicago sativa L.). Exogenous salicylic acid (SA) has been revealed as a cost-effective method of improving defense against freezing stress due to its predominant role in biotic and abiotic stress resistance. However, how the molecular mechanisms of SA improve freezing stress resistance in alfalfa is still unclear. Therefore, in this study, we used leaf samples of alfalfa seedlings pretreatment with 200 μM and 0 μM SA, which were exposed to freezing stress (-10°C) for 0, 0.5, 1, and 2h and allowed to recover at normal temperature in a growth chamber for 2 days, after which we detect the changes in the phenotypical, physiological, hormone content, and performed a transcriptome analysis to explain SA influence alfalfa in freezing stress. The results demonstrated that exogenous SA could improve the accumulation of free SA in alfalfa leaves primarily through the phenylalanine ammonia-lyase pathway. Moreover, the results of transcriptome analysis revealed that the mitogen-activated protein kinase (MAPK) signaling pathway-plant play a critical role in SA alleviating freezing stress. In addition, the weighted gene co-expression network analysis (WGCNA) found that MPK3, MPK9, WRKY22 (downstream target gene of MPK3), and TGACG-binding factor 1 (TGA1) are candidate hub genes involved in freezing stress defense, all of which are involved in the SA signaling pathway. Therefore, we conclude that SA could possibly induce MPK3 to regulate WRKY22 to participate in freezing stress to induced gene expression related to SA signaling pathway (NPR1-dependent pathway and NPR1-independent pathway), including the genes of non-expresser of pathogenesis-related gene 1 (NPR1), TGA1, pathogenesis-related 1 (PR1), superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX), glutathione-S-transferase (GST), and heat shock protein (HSP). This enhanced the production of antioxidant enzymes such as SOD, POD, and APX, which increases the freezing stress tolerance of alfalfa plants.

Transcriptional Regulation of zma-MIR528a by Action of Nitrate and Auxin in Maize

In recent years, miR528, a monocot-specific miRNA, has been assigned multifaceted roles during development and stress response in several plant species. However, the transcription regulation and the molecular mechanisms controlling MIR528 expression in maize are still poorly explored. Here we analyzed the zma-MIR528a promoter region and found conserved transcription factor binding sites related to diverse signaling pathways, including the nitrate (TGA1/4) and auxin (AuxRE) response networks. Accumulation of both pre-miR528a and mature miR528 was up-regulated by exogenous nitrate and auxin treatments during imbibition, germination, and maize seedling establishment. Functional promoter analyses demonstrated that TGA1/4 and AuxRE sites are required for transcriptional induction by both stimuli. Overall, our findings of the nitrogen- and auxin-induced zma-MIR528a expression through cis-regulatory elements in its promoter contribute to the knowledge of miR528 regulome.

CC-type glutaredoxin, MeGRXC3, associates with catalases and negatively regulates drought tolerance in cassava (Manihot esculenta Crantz)

Glutaredoxins (GRXs) are essential for reactive oxygen species (ROS) homeostasis in responses of plants to environment changes. We previously identified several drought-responsive CC-type GRXs in cassava, an important tropical crop. However, how CC-type GRX regulates ROS homeostasis of cassava under drought stress remained largely unknown. Here, we report that a drought-responsive CC-type GRX, namely MeGRXC3, was associated with activity of catalase in the leaves of 100 cultivars (or unique unnamed genotypes) of cassava under drought stress. MeGRXC3 negatively regulated drought tolerance by modulating drought- and abscisic acid-induced stomatal closure in transgenic cassava. It antagonistically regulated hydrogen peroxide (H₂ O₂ ) accumulation in epidermal cells and guard cells. Moreover, MeGRXC3 interacted with two catalases of cassava, MeCAT1 and MeCAT2, and regulated their activity in vivo. Additionally, MeGRXC3 interacts with a cassava TGA transcription factor, MeTGA2, in the nucleus, and regulates the expression of MeCAT7 through a MeTGA2-MeMYB63 pathway. Overall, we demonstrated the roles of MeGRXC3 in regulating activity of catalase at both transcriptional and post-translational levels, therefore involving in ROS homeostasis and stomatal movement in responses of cassava to drought stress. Our study provides the first insights into how MeGRXC3 may be used in molecular breeding of cassava crops.

Analysis of Thioredoxins and Glutaredoxins in Soybean: Evidence of Translational Regulation under Water Restriction

Soybean (Glycine max (L.) Merr.) establishes symbiosis with rhizobacteria, developing the symbiotic nodule, where the biological nitrogen fixation (BNF) occurs. The redox control is key for guaranteeing the establishment and correct function of the BNF process. Plants have many antioxidative systems involved in ROS homeostasis and signaling, among them a network of thio- and glutaredoxins. Our group is particularly interested in studying the differential response of nodulated soybean plants to water-deficit stress. To shed light on this phenomenon, we set up an RNA-seq experiment (for total and polysome-associated mRNAs) with soybean roots comprising combined treatments including the hydric and the nodulation condition. Moreover, we performed the initial identification and description of the complete repertoire of thioredoxins (Trx) and glutaredoxins (Grx) in soybean. We found that water deficit altered the expression of a greater number of differentially expressed genes (DEGs) than the condition of plant nodulation. Among them, we identified 12 thioredoxin (Trx) and 12 glutaredoxin (Grx) DEGs, which represented a significant fraction of the detected GmTrx and GmGrx in our RNA-seq data. Moreover, we identified an enriched network in which a GmTrx and a GmGrx interacted with each other and associated through several types of interactions with nitrogen metabolism enzymes.

TGA factors promote plant root growth by modulating redox homeostasis or response

To identify novel regulators of stem cell renewal, we mined an existing but little explored cell type-specific transcriptome dataset for the Arabidopsis root. A member of the TGA family of transcription factors, TGA8, was found to be specifically expressed in the quiescent center (QC). Mutation in TGA8 caused a subtle root growth phenotype, suggesting functional redundancy with other TGA members. Using a promoter::HGFP transgenic approach, we showed that all TGA factors were expressed in the root, albeit at different levels and with distinct spatial patterns. Mutant analyses revealed that all TGA factors examined contribute to root growth by promoting stem cell renewal, meristem activity, and cell elongation. Combining transcriptome analyses, histochemical assays, and physiological tests, we demonstrated that functional redundancy exists among members of clades II and V or those in clades I and III. These two groups of TGA factors act differently, however, as their mutants responded to oxidative stress differently and quantitative reverse transcription polymerase chain reaction assays showed they regulate different sets of genes that are involved in redox homeostasis. Our study has thus uncovered a previously unrecognized broad role and a mechanistic explanation for TGA factors in root growth and development.

TGA transcription factors-Structural characteristics as basis for functional variability

TGA transcription factors are essential regulators of various cellular processes, their activity connected to different hormonal pathways, interacting proteins and regulatory elements. Belonging to the basic region leucine zipper (bZIP) family, TGAs operate by binding to their target DNA sequence as dimers through a conserved bZIP domain. Despite sharing the core DNA-binding sequence, the TGA paralogues exert somewhat different DNA-binding preferences. Sequence variability of their N- and C-terminal protein parts indicates their importance in defining TGA functional specificity through interactions with diverse proteins, affecting their DNA-binding properties. In this review, we provide a short and concise summary on plant TGA transcription factors from a structural point of view, including the relation of their structural characteristics to their functional roles in transcription regulation.

HbTGA1, a TGA Transcription Factor From Hevea brasiliensis, Regulates the Expression of Multiple Natural Rubber Biosynthesis Genes

The TGA transcription factors are known to modulate the biosynthesis of secondary metabolites in plants. However, their regulatory function in natural rubber (NR) biosynthesis was not revealed in the rubber tree (Hevea brasiliensis). Here, 14 genes encoding TGA transcription factors (name HbTGA1-HbTGA14) were identified in the rubber tree. HbTGAs were differentially expressed in different tissues. HbTGA1 was expressed at its highest level in latex. We found specific in vitro and in vivo binding of the HbTGA1 protein with promoters of multiple NR biosynthesis genes (HbHMGS2, HbHMGR2, HbCPT6, HbCPT8, and HbSRPP2). The activation of the promoters of HbHMGS2 and HbCPT6 was significantly suppressed by HbTGA1, while the activities of promoters of HbHMGR2, HbCPT8, and HbSRPP2 were increased by HbTGA1. The promoter activities of HbHMGS2, HbHMGR2, HbCPT6, HbCPT8, and HbSRPP2 were significantly increased by HbTGA1 under jasmonate stress, while the promoter activities of HbHMGS2, HbHMGR2, HbCPT6, HbCPT8, and HbSRPP2 were also significantly increased by HbTGA1 under salicylic acid stress. The present study provides insights into the role of TGA transcription factors in regulating the expression of NR biosynthesis genes from H. brasiliensis.

OsTGAL1 suppresses the resistance of rice to bacterial blight disease by regulating the expression of salicylic acid glucosyltransferase OsSGT1

Many TGA transcription factors participate in immune responses in the SA-mediated signaling pathway in Arabidopsis. This study identified a transcription factor OsTGAL1, which is induced upon infection by Xoo. Overexpression of OsTGAL1 increased the susceptibility of rice to Xoo. Plants overexpressing OsTGAL1 could affect the expression of many SA signaling-related genes. OsTGAL1 was able to interact with the promoter of OsSGT1, which encodes a key enzyme for SA metabolism. The transcript of OsSGT1 was induced by Xoo and this responsive expression was further increased in plants overexpressing OsTGAL1. OsSGT1 knockout lines had enhanced resistance to Xoo, and knocking out OsSGT1 in plants overexpressing OsTGAL1 blocked the susceptibility caused by OsTGAL1. Altered expression levels of several OsPRs in all the transgenic plants demonstrated that SA-mediated signaling had been affected. Furthermore, we identified an oxidoreductase of CC-type glutaredoxin, OsGRX17, which interacted with OsTGAL1. OsGRX17 reduced the regulation of OsTGAL1 on OsSGT1, and this may be due to its redox modulation. Thus, our results demonstrate that OsTGAL1 negatively regulates resistance to Xoo by its effects on SA metabolism via the activation of OsSGT1, which provides valuable targets for plant breeders in developing new cultivars that are resistant to Xoo.

The soybean TGA transcription factor GmTGA13 plays important roles in the response to salinity stress

Soybean (Glycine max L.) is an important oil, food and economic crop in the world. High salinity severely affects the growth and yield of soybean. Overexpressing a specific anti-retroviral transcription factor by biotechnology is an effective way to cultivate new stress-tolerant varieties of soybean. TGA transcription factor is a subfamily of bZIP and plays an important role in abiotic stress responses. A TGA subfamily gene GmTGA13 was cloned and the gene expression, subcellular localization and transcriptional activity were measured. Through the Ag. tumefaciens mediated flower dip method and the Ag. rhizogenes mediated transformation of soybean hairy roots, the transgenic Arabidopsis and the 'combination' soybean plants of overexpressing GmTGA13 were obtained. The two types of transgenic plants were treated with salt stress respectively, and the related physiological indexes were determined. Furthermore, the expression levels of five abiotic stress responsive genes were analyzed in GmTGA13 overexpression hairy roots. GmTGA13 gene was highly expressed in roots and significantly induced by saline stress in soybean. GmTGA13 encoded a nuclear localization protein and had transcriptional activation activity. Overexpression of GmTGA13 enhanced the saline stress tolerance of transgenic Arabidopsis and the 'combination' soybean plants. Furthermore, overexpression of GmTGA13 enhanced the expression of the stress responsive genes in transgenic soybean hairy roots. In conclusion, overexpression of GmTGA13 is beneficial to the absorption of K+ and Ca2+ by the cell, thereby regulating the ion homeostasis in the cell balance. GmTGA13 enhanced salt resistance of plants by regulating the expression of many stress-responsive genes.

Role of cassava CC-type glutaredoxin MeGRXC3 in regulating sensitivity to mannitol-induced osmotic stress dependent on its nuclear activity

BACKGROUND

We previously identified six drought-inducible CC-type glutaredoxins in cassava cultivars, however, less is known about their potential role in the molecular mechanism by which cassava adapted to abiotic stress.

RESULTS

Herein, we investigate one of cassava drought-responsive CC-type glutaredoxins, namely MeGRXC3, that involved in regulation of mannitol-induced inhibition on seed germination and seedling growth in transgenic Arabidopsis. MeGRXC3 overexpression up-regulates several stress-related transcription factor genes, such as PDF1.2, ERF6, ORA59, DREB2A, WRKY40, and WRKY53 in Arabidopsis. Protein interaction assays show that MeGRXC3 interacts with Arabidopsis TGA2 and TGA5 in the nucleus. Eliminated nuclear localization of MeGRXC3 failed to result mannitol-induced inhibition of seed germination and seedling growth in transgenic Arabidopsis. Mutation analysis of MeGRXC3 indicates the importance of conserved motifs for its transactivation activity in yeast. Additionally, these motifs are also indispensable for its functionality in regulating mannitol-induced inhibition of seed germination and enhancement of the stress-related transcription factors in transgenic Arabidopsis.

CONCLUSIONS

MeGRXC3 overexpression confers mannitol sensitivity in transgenic Arabidopsis possibly through interaction with TGA2/5 in the nucleus, and nuclear activity of MeGRXC3 is required for its function.

Glutaredoxins regulate maize inflorescence meristem development via redox control of TGA transcriptional activity

Glutaredoxins (GRXs) are small oxidoreductases that can modify target protein activities through control of the redox (reduction/oxidation) state by reducing or glutathionylating disulfide bridges. Although CC-type GRXs are plant specific and play important roles in many processes, the mechanisms by which they modulate the activity of target proteins in vivo are unknown. In this study, we show that a maize CC-type GRX, MALE STERILE CONVERTED ANTHER1 (MSCA1), acts redundantly with two paralogues, ZmGRX2 and ZmGRX5, to modify the redox state and the activity of its putative target, the TGA transcription factor FASCIATED EAR4 (FEA4) that acts as a negative regulator of inflorescence meristem development. We used CRISPR-Cas9 to create a GRX triple knockout, resulting in severe suppression of meristem, ear and tassel growth and reduced plant height. We further show that GRXs regulate the redox state, DNA accessibility and transcriptional activities of FEA4, which acts downstream of MSCA1 and its paralogues to control inflorescence development. Our findings reveal the function of GRXs in meristem development, and also provide direct evidence for GRX-mediated redox modification of target proteins in plants.

Meta-analysis of transcriptomic studies of cytokinin-treated rice roots defines a core set of cytokinin response genes

Cytokinins regulate diverse aspects of plant growth and development, primarily through modulation of gene expression. The cytokinin-responsive transcriptome has been thoroughly described in dicots, especially Arabidopsis, but much less so in monocots. Here, we present a meta-analysis of five different transcriptomic analyses of rice (Oryza sativa) roots treated with cytokinin, including three previously unpublished experiments. We developed a treatment method in which hormone is added to the media of rice seedlings grown in sterile hydroponic culture under a continuous airflow, which resulted in minimal perturbation of the seedlings, thus greatly reducing changes in gene expression in the absence of exogenous hormone. We defined a core set of 205 upregulated and 86 downregulated genes that were differentially expressed in at least three of the transcriptomic datasets. This core set includes genes encoding the type-A response regulators (RRs) and cytokinin oxidases/dehydrogenases, which have been shown to be primary cytokinin response genes. GO analysis revealed that the upregulated genes were enriched for terms related to cytokinin/hormone signaling and metabolism, while the downregulated genes were significantly enriched for genes encoding transporters. Variations of type-B RR binding motifs were significantly enriched in the promoters of the upregulated genes, as were binding sites for other potential partner transcription factors. The promoters of the downregulated genes were generally enriched for distinct cis-acting motifs and did not include the type-B RR binding motif. This analysis provides insight into the molecular mechanisms underlying cytokinin action in a monocot and provides a useful foundation for future studies of this hormone in rice and other cereals.

Genome-Wide Identification of Populus Malectin/Malectin-Like Domain-Containing Proteins and Expression Analyses Reveal Novel Candidates for Signaling and Regulation of Wood Development

Malectin domain (MD) is a ligand-binding protein motif of pro- and eukaryotes. It is particularly abundant in Viridiplantae, where it occurs as either a single (MD, PF11721) or tandemly duplicated domain (PF12819) called malectin-like domain (MLD). In herbaceous plants, MD- or MLD-containing proteins (MD proteins) are known to regulate development, reproduction, and resistance to various stresses. However, their functions in woody plants have not yet been studied. To unravel their potential role in wood development, we carried out genome-wide identification of MD proteins in the model tree species black cottonwood (Populus trichocarpa), and analyzed their expression and co-expression networks. P. trichocarpa had 146 MD genes assigned to 14 different clades, two of which were specific to the genus Populus. 87% of these genes were located on chromosomes, the rest being associated with scaffolds. Based on their protein domain organization, and in agreement with the exon-intron structures, the MD genes identified here could be classified into five superclades having the following domains: leucine-rich repeat (LRR)-MD-protein kinase (PK), MLD-LRR-PK, MLD-PK (CrRLK1L), MLD-LRR, and MD-Kinesin. Whereas the majority of MD genes were highly expressed in leaves, particularly under stress conditions, eighteen showed a peak of expression during secondary wall formation in the xylem and their co-expression networks suggested signaling functions in cell wall integrity, pathogen-associated molecular patterns, calcium, ROS, and hormone pathways. Thus, P. trichocarpa MD genes having different domain organizations comprise many genes with putative foliar defense functions, some of which could be specific to Populus and related species, as well as genes with potential involvement in signaling pathways in other tissues including developing wood.

β-aminobutyric acid induces priming defence against Botrytis cinerea in grapefruit by reducing intercellular redox status that modifies posttranslation of VvNPR1 and its interaction with VvTGA1

Either NPR1 or TGA1 serve as master redox-sensitive transcriptional regulators for the transcription of PR genes in plants. The redox modification of the two co-activators involved in BABA-induced priming resistance against Botrytis cinerea in grapes was examined in this study. The results showed that 10 mmol L^-1 BABA could effectively trigger a priming defense in grapes as manifested by augmented expression levels of PR genes upon inoculation with B. cinerea. Moreover, transcriptome profiling analysis revealed that all of the sets of key genes in the enzymatic ROS scavenging system, the PPP and AsA-GSH cycle were in harmony and were transcriptionally induced in BABA-primed grapes with pathogenic infection; in addition, this enhanced expression caused the accelerated accumulation of reductive substances, namely, AsA, GSH and NADPH, resulting in reduced intercellular conditions. Under reduced conditions, the interaction of VvTGA1 and VvNPR1 in the Y2H assay implied that VvTGA1 can provide the DNA binding capacity required by VvNPR1 for activation of VvPR genes. Consequently, the transactivation of VvNPR1 by the promoters of VvPR1, VvPR2 and VvPR5 was determined via a DLR assay, and it induced the transcription of the VvPR genes. In parallel, the redox-modified reducing condition achieved with an abundant supply of reductive substances was closely associated with the translocation of NPR1 for interaction with TGA in the nucleus. Thus, the posttranslational modification and subsequent interaction of the two redox-sensitive co-activators of VvNPR1 and VvTGA1 under reduced conditions may be responsible for BABA-induced priming for effective disease resistance in grapes.

Glutaredoxin AtGRXS8 represses transcriptional and developmental responses to nitrate in Arabidopsis thaliana roots

Glutaredoxins (GRXs) are small oxidoreductase enzymes that can reduce disulfide bonds in target proteins. The class III GRX gene family is unique to land plants, and Arabidopsis thaliana has 21 class III GRXs, which remain largely uncharacterized. About 80% of A. thaliana class III GRXs are transcriptionally regulated by nitrate, and several recent studies have suggested roles for these GRXs in nitrogen signaling. Our objective was to functionally characterize two nitrate-induced GRX genes, AtGRXS5 and AtGRXS8, defining their roles in signaling and development in the A. thaliana root. We demonstrated that AtGRXS5 and AtGRXS8 are primarily expressed in root and shoot vasculature (phloem), and that the corresponding GRX proteins display nucleo-cytosolic subcellular localization. Ectopic expression of AtGRXS8 in transgenic plants caused major alterations in root system architecture: Normal primary root development, but a near absence of lateral roots. RNA sequencing demonstrated that the roots of AtGRXS8-overexpressing plants show strongly reduced transcript abundance for many primary nitrate response genes, including the major high-affinity nitrate transporters. Correspondingly, high-affinity nitrate uptake and the transport of nitrate from roots to shoots are compromised in AtGRXS8-overexpressing plants. Finally, we demonstrated that the AtGRXS8 protein can physically interact with the TGA1 and TGA4 transcription factors, which are central regulators of early transcriptional responses to nitrate in A. thaliana roots. Overall, these results suggest that AtGRXS8 acts to quench both transcriptional and developmental aspects of primary nitrate response, potentially by interfering with the activity of the TGA1 and TGA4 transcription factors.

Transcriptomic analysis of poco1, a mitochondrial pentatricopeptide repeat protein mutant in Arabidopsis thaliana

BACKGROUND

Flowering is a crucial stage during plant development. Plants may respond to unfavorable conditions by accelerating reproductive processes like flowering. In a recent study, we showed that PRECOCIOUS1 (POCO1) is a mitochondrial pentatricopeptide repeat (PPR) protein involved in flowering time and abscisic acid (ABA) signaling in Arabidopsis thaliana. Here, we use RNA-seq data to investigate global gene expression alteration in the poco1 mutant.

RESULTS

RNA-seq analysis was performed during different developmental stages for wild-type and poco1 plants. The most profound differences in gene expression were found when wild-type and poco1 plants of the same developmental stage were compared. Coverage analysis confirmed the T-DNA insertion in POCO1, which was concomitant with truncated transcripts. Many biological processes were found to be enriched. Several flowering-related genes such as FLOWERING LOCUS T (FT), which may be involved in the early-flowering phenotype of poco1, were differentially regulated. Numerous ABA-associated genes, including the core components of ABA signaling such as ABA receptors, protein phosphatases, protein kinases, and ABA-responsive element (ABRE) binding proteins (AREBs)/ABRE-binding factors (ABFs) as well as important genes for stomatal function, were mostly down-regulated in poco1. Drought and oxidative stress-related genes, including ABA-induced stress genes, were differentially regulated. RNA-seq analysis also uncovered differentially regulated genes encoding various classes of transcription factors and genes involved in cellular signaling. Furthermore, the expression of stress-associated nuclear genes encoding mitochondrial proteins (NGEMPs) was found to be altered in poco1. Redox-related genes were affected, suggesting that the redox state in poco1 might be altered.

CONCLUSION

The identification of various enriched biological processes indicates that complex regulatory mechanisms underlie poco1 development. Differentially regulated genes associated with flowering may contribute to the early-flowering phenotype of poco1. Our data suggest the involvement of POCO1 in the early ABA signaling process. The down-regulation of many ABA-related genes suggests an association of poco1 mutation with the ABA signaling deficiency. This condition further affects the expression of many stress-related, especially drought-associated genes in poco1, consistent with the drought sensitivity of poco1. poco1 mutation also affects the expression of genes associated with the cellular regulation, redox, and mitochondrial perturbation.

Molecular Rewiring of the Jasmonate Signaling Pathway to Control Auxin-Responsive Gene Expression

The plant hormone jasmonic acid (JA) has an important role in many aspects of plant defense response and developmental process. JA triggers interaction between the F-box protein COI1 and the transcriptional repressors of the JAZ family that leads the later to proteasomal degradation. The Jas-motif of JAZs is critical for mediating the COI1 and JAZs interaction in the presence of JA. Here, by using the protoplast transient gene expression system we reported that the Jas-motif of JAZ1 was necessary and sufficient to target a foreign reporter protein for COI1-facilitated degradation. We fused the Jas-motif to the SHY2 transcriptional repressor of auxin signaling pathway to create a chimeric protein JaSHY. Interestingly, JaSHY retained the transcriptional repressor function while become degradable by the JA coreceptor COI1 in a JA-dependent fashion. Moreover, the JA-induced and COI1-facilitated degradation of JaSHY led to activation of a synthetic auxin-responsive promoter activity. These results showed that the modular components of JA signal transduction pathway can be artificially redirected to regulate auxin signaling pathway and control auxin-responsive gene expression. Our work provides a general strategy for using synthetic biology approaches to explore and design cell signaling networks to generate new cellular functions in plant systems.

Reconstitution of the Jasmonate Signaling Pathway in Plant Protoplasts

The phytohormone jasmonic acid (JA) plays an important role in various plant developmental processes and environmental adaptations. The JA signaling pathway has been well-elucidated in the reference plant Arabidopsis thaliana. It starts with the perception of the active JA derivative, jasmonoyl-isoleucine (JA-Ile), by the F-box protein COI1 which is part of the E3-ligase SCF^COI1. Binding of JA-Ile enables the interaction between COI1 and JAZ repressor proteins. Subsequent degradation of JAZ proteins leads to the activation of transcription factors like e.g., MYC2. Here we demonstrate that the pathway can be reconstituted in transiently transformed protoplasts. Analysis of the stability of a JAZ1-fLuc fusion protein as a function of COI1 transiently expressed in coi1 protoplasts allows structure function analysis of both JAZs and COI1. Using this system, we found that conserved cysteines in COI1 influence steady state COI1 protein levels. Using a luciferase reporter gene under the control of the JAZ1 promoter enable to address those features of JAZ1 that are required for MYC2 repression. Interestingly, the conserved TIFY-motif previously described to interact with NINJA to recruit the corepressor TOPLESS is not necessary for repression. This result is in favor of the alternative repression mode that proposes a direct competition between repressive JAZs and promotive MEDIATOR25 at MYC2. Finally, using protoplasts from the aos coi1 double mutant, which is deficient in JA synthesis and perception, we provide a system that has the potential to study the activity of different COI1 variants in the presence of different ligands.