The Arabidopsis bZIP gene AtbZIP63 is a sensitive integrator of transient abscisic acid and glucose signals

In-Depth Characterization of bZIP Genes in the Context of Endoplasmic Reticulum (ER) Stress in Brassica campestris ssp. chinensis

Numerous studies have been conducted to investigate the genomic characterization of bZIP genes and their involvement in the cellular response to endoplasmic reticulum (ER) stress. These studies have provided valuable insights into the coordinated cellular response to ER stress, which is mediated by bZIP transcription factors (TFs). However, a comprehensive and systematic investigations regarding the role of bZIP genes and their involvement in ER stress response in pak choi is currently lacking in the existing literature. To address this knowledge gap, the current study was initiated to elucidate the genomic characteristics of bZIP genes, gain insight into their expression patterns during ER stress in pak choi, and investigate the protein-to-protein interaction of bZIP genes with the ER chaperone BiP. In total, 112 members of the BcbZIP genes were identified through a comprehensive genome-wide analysis. Based on an analysis of sequence similarity, gene structure, conserved domains, and responsive motifs, the identified BcbZIP genes were categorized into 10 distinct subfamilies through phylogenetic analysis. Chromosomal location and duplication events provided insight into their genomic context and evolutionary history. Divergence analysis estimated their evolutionary history with a predicted divergence time ranging from 0.73 to 80.71 million years ago (MYA). Promoter regions of the BcbZIP genes were discovered to exhibit a wide variety of cis-elements, including light, hormone, and stress-responsive elements. GO enrichment analysis further confirmed their roles in the ER unfolded protein response (UPR), while co-expression network analysis showed a strong relationship of BcbZIP genes with ER-stress-responsive genes. Moreover, gene expression profiles and protein-protein interaction with ER chaperone BiP further confirmed their roles and capacity to respond to ER stress in pak choi.

Wheat bZIPC1 interacts with FT2 and contributes to the regulation of spikelet number per spike

KEY MESSAGE

The wheat transcription factor bZIPC1 interacts with FT2 and affects spikelet and grain number per spike. We identified a natural allele with positive effects on these two economically important traits. Loss-of-function mutations and natural variation in the gene FLOWERING LOCUS T2 (FT2) in wheat have previously been shown to affect spikelet number per spike (SNS). However, while other FT-like wheat proteins interact with bZIP-containing transcription factors from the A-group, FT2 does not interact with any of them. In this study, we used a yeast-two-hybrid screen with FT2 as bait and identified a grass-specific bZIP-containing transcription factor from the C-group, designated here as bZIPC1. Within the C-group, we identified four clades including wheat proteins that show Y2H interactions with different sets of FT-like and CEN-like encoded proteins. bZIPC1 and FT2 expression partially overlap in the developing spike, including the inflorescence meristem. Combined loss-of-function mutations in bZIPC-A1 and bZIPC-B1 (bzipc1) in tetraploid wheat resulted in a drastic reduction in SNS with a limited effect on heading date. Analysis of natural variation in the bZIPC-B1 (TraesCS5B02G444100) region revealed three major haplotypes (H1-H3), with the H1 haplotype showing significantly higher SNS, grain number per spike and grain weight per spike than both the H2 and H3 haplotypes. The favorable effect of the H1 haplotype was also supported by its increased frequency from the ancestral cultivated tetraploids to the modern tetraploid and hexaploid wheat varieties. We developed markers for the two non-synonymous SNPs that differentiate the bZIPC-B1b allele in the H1 haplotype from the ancestral bZIPC-B1a allele present in all other haplotypes. These diagnostic markers are useful tools to accelerate the deployment of the favorable bZIPC-B1b allele in pasta and bread wheat breeding programs.

Auxin and abscisic acid play important roles in promoting glucose metabolism of reactivated young kernels of maize (Zea mays L.)

In maize, young kernels that are less competitive and have poor sink activity often abort. Studies have indicated that such poor competitiveness depends, in part, on the regulation by auxin (IAA) and abscisic acid (ABA). However, the mechanisms for such effects remain unclear. We used pollination-blocking and hand-pollination treatments accompanied by multi-omics and physiological tests, to identify underlying mechanism by which IAA and ABA, along with sugar signaling affect kernel development. Results showed that preventing pollination of the primary ears reactivated kernels in the secondary ears and altered both sugar metabolism and hormone signaling pathways. This was accompanied by increased enzyme activities in carbon metabolism and concentrations of glucose and starch, as well as increased levels of IAA and decreased levels of ABA in the reactivated kernels. Positive and negative correlations were observed between IAA, ABA contents and cell wall invertase (CWIN) activity, and glucose contents, respectively. In vitro culture revealed that the expression of genes involved in glucose utilization was upregulated by IAA, but downregulated by ABA. IAA could promote the expression of ABA signaling genes ZmPP2C9 and ZmPP2C13 but downregulated the expression of Zmnced5, an ABA biosynthesis gene, and ZmSnRK2.10, which is involved in ABA signal transduction. However, these genes showed opposite trends when IAA transport was inhibited. To summarize, we suggest a regulatory model for how IAA inhibits ABA metabolism by promoting the smooth utilization of glucose in reactivated young kernels. Our findings highlight the importance of IAA in ABA signaling by regulating glucose production and transport in maize.

Transcriptomic Analysis of Differentially Expressed Genes in Arabidopsis thaliana Overexpressing BnMYB2 from Boehmeria nivea under Cadmium Stress

Boehmeria nivea (ramie) is an important fiber crop with strong tolerance to cadmium (Cd). In our previous study, a novel MYB transcription factor gene from ramie, BnMYB2, was found to positively regulate Cd tolerance and accumulation in the transgenic Arabidopsis thaliana lines. Herein, transcriptome sequencing was performed to identify the differentially expressed genes involved in cadmium response between the wild-type (WT) and BnMYB2 overexpressed lines; 1598 differentially expressed genes (DEGs) were detected in the shoot. GO and KEGG analysis indicated that the majority of DEGs belonged to the categories of transcription factors, plant hormone signal transduction and nitrogen metabolism. The expression level of the Ib subgroup bHLH genes (AtbHLH38, AtbHLH39, AtbHLH100 and AtbHLH101) and nitrogen assimilation-related genes (AtNIA1, AtNIA2, AtNIR1 and AtASN2) were significantly higher than that of WT, accompanied with the positive changes in iron (Fe) and total nitrogen content in the shoot of BnMYB2 overexpression lines. Several DEGs belonging to the bZIP transcription factor family or SAUR family were also found up-regulated in the transgenic plants. These results provide important clues for elucidating how the molecular mechanisms of BnMYB2 regulate plant response to Cd stress.

SPINDLY O-fucosylates nuclear and cytoplasmic proteins involved in diverse cellular processes in plants

SPINDLY (SPY) is a novel nucleocytoplasmic protein O-fucosyltransferase that regulates target protein activity or stability via O-fucosylation of specific Ser/Thr residues. Previous genetic studies indicate that AtSPY regulates plant development during vegetative and reproductive growth by modulating gibberellin and cytokinin responses. AtSPY also regulates the circadian clock and plant responses to biotic and abiotic stresses. The pleiotropic phenotypes of spy mutants point to the likely role of AtSPY in regulating key proteins functioning in diverse cellular pathways. However, very few AtSPY targets are known. Here, we identified 88 SPY targets from Arabidopsis (Arabidopsis thaliana) and Nicotiana benthamiana via the purification of O-fucosylated peptides using Aleuria aurantia lectin followed by electron transfer dissociation-MS/MS analysis. Most AtSPY targets were nuclear proteins that function in DNA repair, transcription, RNA splicing, and nucleocytoplasmic transport. Cytoplasmic AtSPY targets were involved in microtubule-mediated cell division/growth and protein folding. A comparison with the published O-linked-N-acetylglucosamine (O-GlcNAc) proteome revealed that 30% of AtSPY targets were also O-GlcNAcylated, indicating that these distinct glycosylations could co-regulate many protein functions. This study unveiled the roles of O-fucosylation in modulating many key nuclear and cytoplasmic proteins and provided a valuable resource for elucidating the regulatory mechanisms involved.

WRKY transcription factors: evolution, regulation, and functional diversity in plants

The recent advancements in sequencing technologies and informatic tools promoted a paradigm shift to decipher the hidden biological mysteries and transformed the biological issues into digital data to express both qualitative and quantitative forms. The transcriptomic approach, in particular, has added new dimensions to the versatile essence of plant genomics through the large and deep transcripts generated in the process. This has enabled the mining of super families from the sequenced plants, both model and non-model, understanding their ancestry, diversity, and evolution. The elucidation of the crystal structure of the WRKY proteins and recent advancement in computational prediction through homology modeling and molecular dynamic simulation has provided an insight into the DNA-protein complex formation, stability, and interaction, thereby giving a new dimension in understanding the WRKY regulation. The present review summarizes the functional aspects of the high volume of sequence data of WRKY transcription factors studied from different species, till date. The review focuses on the dynamics of structural classification and lineage in light of the recent information. Additionally, a comparative analysis approach was incorporated to understand the functions of the identified WRKY transcription factors subjected to abiotic (heat, cold, salinity, senescence, dark, wounding, UV, and carbon starvation) stresses as revealed through various sets of studies on different plant species. The review will be instrumental in understanding the events of evolution and the importance of WRKY TFs under the threat of climate change, considering the new scientific evidences to propose a fresh perspective.

Basic helix-loop-helix transcription factor PxbHLH02 enhances drought tolerance in Populus (Populus simonii × P. nigra)

The basic helix-loop-helix (bHLH) transcription factors (TFs) are involved in plant morphogenesis and various abiotic and biotic stress responses. However, further exploration is required of drought-responsive bHLH family members and their detailed regulatory mechanisms in Populus. Two bHLH TF genes, PxbHLH01/02, were identified in Populus simonii × P. nigra and cloned. The aim of this study was to examine the role of bHLH TFs in drought tolerance in P. simonii × P. nigra. The results showed that the amino acid sequences of the two genes were homologous to Arabidopsis thaliana UPBEAT1 (AtUPB1) and overexpression of PxbHLH01/02 restored normal root length in the AtUPB1 insertional mutant (upb1-1). The PxbHLH01/02 gene promoter activity analysis suggested that they were involved in stress responses and hormone signaling. Furthermore, Arabidopsis transgenic lines overexpressing PxbHLH01/02 exhibited higher stress tolerance compared with the wild-type. Populus simonii × P. nigra overexpressing PxbHLH02 increased drought tolerance and exhibited higher superoxide dismutase and peroxidase activities, lower H2O2 and malondialdehyde content, and lower relative conductivity. The results of transcriptome sequencing (RNA-seq) and quantitative real-time PCR suggested that the response of PxbHLH02 to drought stress was related to abscisic acid (ABA) signal transduction. Overall, the findings of this study suggest that PxbHLH02 from P. simonii × P. nigra functions as a positive regulator of drought stress responses by regulating stomatal aperture and promoting ABA signal transduction.

Altering the balance between AOX1A and NDB2 expression affects a common set of transcripts in Arabidopsis

Stress-responsive components of the mitochondrial alternative electron transport pathway have the capacity to improve tolerance of plants to abiotic stress, particularly the alternative oxidase AOX1A but also external NAD(P)H dehydrogenases such as NDB2, in Arabidopsis. NDB2 and AOX1A can cooperate to entirely circumvent the classical electron transport chain in Arabidopsis mitochondria. Overexpression of AOX1A or NDB2 alone can have slightly negative impacts on plant growth under optimal conditions, while simultaneous overexpression of NDB2 and AOX1A can reverse these phenotypic effects. We have taken a global transcriptomic approach to better understand the molecular shifts that occur due to overexpression of AOX1A alone and with concomitant overexpression of NDB2. Of the transcripts that were significantly up- or down- regulated in the AOX1A overexpression line compared to wild type (410 and 408, respectively), the majority (372 and 337, respectively) reverted to wild type levels in the dual overexpression line. Several mechanisms for the AOX1A overexpression phenotype are proposed based on the functional classification of these 709 genes, which can be used to guide future experiments. Only 28 genes were uniquely up- or down-regulated when NDB2 was overexpressed in the AOX1A overexpression line. On the other hand, many unique genes were deregulated in the NDB2 knockout line. Furthermore, several changes in transcript abundance seen in the NDB2 knockout line were consistent with changes in the AOX1A overexpression line. The results suggest that an imbalance in AOX1A:NDB2 protein levels caused by under- or over-expression of either component, triggers a common set of transcriptional responses that may be important in mitochondrial redox regulation. The most significant changes were transcripts associated with photosynthesis, secondary metabolism and oxidative stress responses.

The double knockdown of the mitochondrial uncoupling protein isoforms reveals partial redundant roles during Arabidopsis thaliana vegetative and reproductive development

Mitochondrial uncoupling proteins (UCPs) are specialized proteins capable of dissipating the proton electrochemical gradient generated in respiration independent of ATP synthesis. Three UCP coding genes with distinct expression patterns have been identified in Arabidopsis thaliana (namely UCP1, UCP2 and UCP3). Here, we generated T-DNA double-insertion mutants (ucp1 ucp2, ucp1 ucp3 and ucp2 ucp3) to investigate the functionality of the Arabidopsis UCP isoforms. A strong compensatory effect of the wild-type UCP gene was found in the double-knockdown lines. Higher levels of reactive oxygen species (ROS) were observed in vegetative and reproductive organs of double mutant plants. This exacerbated oxidative stress in plants also increased lipid peroxidation but was not compensated by the activation of the antioxidant system. Alterations in O₂ consumption and ADP/ATP ratio were also observed, suggesting a change in mitochondrial energy-generating processes. Deficiencies in double-mutants were not limited to mitochondria and also changed photosynthetic efficiency and redox state. Our results indicate that UCP2 and UCP3 have complementary function with UCP1 in plant reproductive and vegetative organ/tissues, as well as in stress adaptation. The partial redundancy between the UCP isoforms suggests that they could act separately or jointly on mitochondrial homeostasis during A. thaliana development.

Energy homeostasis mediated by the LcSnRK1α-LcbZIP1/3 signaling pathway modulates litchi fruit senescence

Cellular energy status is a key factor deciding the switch-on of the senescence of horticultural crops. Despite the established significance of the conserved energy master regulator sucrose non-fermenting 1 (SNF1)-related protein kinase 1 (SnRK1) in plant development, its working mechanism and related signaling pathway in the regulation of fruit senescence remain enigmatic. Here, we demonstrate that energy deficit accelerates fruit senescence, whereas exogenous ATP treatment delays it. The transient suppression of LcSnRK1α in litchi (Litchi chinensis Sonn.) fruit inhibited the expression of energy metabolism-related genes, while its ectopic expression in tomato (Solanum lycopersicum) promoted ripening and a high energy level. Biochemical analyses revealed that LcSnRK1α interacted with and phosphorylated the transcription factors LcbZIP1 and LcbZIP3, which directly bound to the promoters to activate the expression of DARK-INDUCIBLE 10 (LcDIN10), ASPARAGINE SYNTHASE 1 (LcASN1), and ANTHOCYANIN SYNTHASE (LcANS), thereby fine-tuning the metabolic reprogramming to ensure energy and redox homeostasis. Altogether, these observations reveal a post-translational modification mechanism by which LcSnRK1α-mediated phosphorylation of LcbZIP1 and LcbZIP3 regulates the expression of metabolic reprogramming-related genes, consequently modulating litchi fruit senescence.

Sugar metabolism during pre- and post-fertilization events in plants under high temperature stress

High temperature challenges global crop production by limiting the growth and development of the reproductive structures and seed. It impairs the developmental stages of male and female gametogenesis, pollination, fertilization, endosperm formation and embryo development. Among these, the male reproductive processes are highly prone to abnormalities under high temperature at various stages of development. The disruption of source-sink balance is the main constraint for satisfactory growth of the reproductive structures which is disturbed at the level of sucrose import and utilization within the tissue. Seed development after fertilization is affected by modulation in the activity of enzymes involved in starch metabolism. In addition, the alteration in the seed-filling rate and its duration affects the seed weight and quality. The present review critically discusses the role of sugar metabolism in influencing the various stages of gamete and seed development under high temperature stress. It also highlights the interaction of the sugars with hormones that mediate the transport of sugars to sink tissues. The role of transcription factors for the regulation of sugar availability under high temperature has also been discussed. Further, the omics-based systematic investigation has been suggested to understand the synergistic or antagonistic interactions between sugars, hormones and reactive oxygen species at various points of sucrose flow from source to sink under high temperature stress.

The evolutionarily conserved kinase SnRK1 orchestrates resource mobilization during Arabidopsis seedling establishment

The onset of plant life is characterized by a major phase transition. During early heterotrophic seedling establishment, seed storage reserves fuel metabolic demands, allowing the plant to switch to autotrophic metabolism. Although metabolic pathways leading to storage compound mobilization are well-described, the regulatory circuits remain largely unresolved. Using an inducible knockdown approach of the evolutionarily conserved energy master regulator Snf1-RELATED-PROTEIN-KINASE1 (SnRK1), phenotypic studies reveal its crucial function in Arabidopsis thaliana seedling establishment. Importantly, glucose feeding largely restores growth defects of the kinase mutant, supporting its major impact in resource mobilization. Detailed metabolite studies reveal sucrose as a primary resource early in seedling establishment, in a SnRK1-independent manner. Later, SnRK1 orchestrates catabolism of triacylglycerols and amino acids. Concurrent transcriptomic studies highlight SnRK1 functions in controlling metabolic hubs fuelling gluconeogenesis, as exemplified by cytosolic PYRUVATE ORTHOPHOSPHATE DIKINASE (cyPPDK). Here, SnRK1 establishes its function via phosphorylation of the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63), which directly targets and activates the cyPPDK promoter. Taken together, our results disclose developmental and catabolic functions of SnRK1 in seed storage mobilization and describe a prototypic gene regulatory mechanism. As seedling establishment is important for plant vigor and crop yield, our findings are of agronomical importance.

Turning the Knobs: The Impact of Post-translational Modifications on Carbon Metabolism

Plants rely on the carbon fixed by photosynthesis into sugars to grow and reproduce. However, plants often face non-ideal conditions caused by biotic and abiotic stresses. These constraints impose challenges to managing sugars, the most valuable plant asset. Hence, the precise management of sugars is crucial to avoid starvation under adverse conditions and sustain growth. This review explores the role of post-translational modifications (PTMs) in the modulation of carbon metabolism. PTMs consist of chemical modifications of proteins that change protein properties, including protein-protein interaction preferences, enzymatic activity, stability, and subcellular localization. We provide a holistic view of how PTMs tune resource distribution among different physiological processes to optimize plant fitness.

How Stress Affects Your Budget-Stress Impacts on Starch Metabolism

Starch is a polysaccharide that is stored to be used in different timescales. Transitory starch is used during nighttime when photosynthesis is unavailable. Long-term starch is stored to support vegetative or reproductive growth, reproduction, or stress responses. Starch is not just a reserve of energy for most plants but also has many other roles, such as promoting rapid stomatal opening, making osmoprotectants, cryoprotectants, scavengers of free radicals and signals, and reverting embolised vessels. Biotic and abiotic stress vary according to their nature, strength, duration, developmental stage of the plant, time of the day, and how gradually they develop. The impact of stress on starch metabolism depends on many factors: how the stress impacts the rate of photosynthesis, the affected organs, how the stress impacts carbon allocation, and the energy requirements involved in response to stress. Under abiotic stresses, starch degradation is usually activated, but starch accumulation may also be observed when growth is inhibited more than photosynthesis. Under biotic stresses, starch is usually accumulated, but the molecular mechanisms involved are largely unknown. In this mini-review, we explore what has been learned about starch metabolism and plant stress responses and discuss the current obstacles to fully understanding their interactions.

Knockdown of Mitochondrial Uncoupling Proteins 1 and 2 (AtUCP1 and 2) in Arabidopsis thaliana Impacts Vegetative Development and Fertility

Mitochondrial uncoupling proteins (UCPs) are mitochondrial inner membrane proteins that dissipate the proton electrochemical gradient generated by the respiratory chain complexes. In plants, these proteins are crucial for maintaining mitochondrial reactive oxygen species (ROS) homeostasis. In this study, single T-DNA insertion mutants for two (AtUCP1 and AtUCP2) out of the three UCP genes present in Arabidopsis thaliana were employed to elucidate their potential roles in planta. Our data revealed a significant increase in the Adenosine triphosphate (ATP)/Adenosine diphosphate (ADP) ratios of both mutants, indicating clear alterations in energy metabolism, and a reduced respiratory rate in atucp2. Phenotypic characterization revealed that atucp1 and atucp2 plants displayed reduced primary root growth under normal and stressed conditions. Moreover, a reduced fertility phenotype was observed in both mutants, which exhibited an increased number of sterile siliques and a lower seed yield compared with wild-type plants. Reciprocal crosses demonstrated that both male fertility and female fertility were compromised in atucp1, while such effect was exclusively observed in the male counterpart in atucp2. Most strikingly, a pronounced accumulation of hydrogen peroxide in the reproductive organs was observed in all mutant lines, indicating a disturbance in ROS homeostasis of mutant flowers. Accordingly, the atucp1 and atucp2 mutants exhibited higher levels of ROS in pollen grains. Further, alternative oxidase 1a was highly induced in mutant flowers, while the expression profiles of transcription factors implicated in gene regulation during female and male reproductive organ/tissue development were perturbed. Overall, these data support the important role for AtUCP1 and AtUCP2 in flower oxidative homeostasis and overall plant fertility.

Genome-wide dynamic network analysis reveals the potential genes for MeJA-induced growth-to-defense transition

BACKGROUND

Methyl jasmonate (MeJA), which has been identified as a lipid-derived stress hormone, mediates plant resistance to biotic/abiotic stress. Understanding MeJA-induced plant defense provides insight into how they responding to environmental stimuli.

RESULT

In this work, the dynamic network analysis method was used to quantitatively identify the tipping point of growth-to-defense transition and detect the associated genes. As a result, 146 genes were detected as dynamic network biomarker (DNB) members and the critical defense transition was identified based on dense time-series RNA-seq data of MeJA-treated Arabidopsis thaliana. The GO functional analysis showed that these DNB genes were significantly enriched in defense terms. The network analysis between DNB genes and differentially expressed genes showed that the hub genes including SYP121, SYP122, WRKY33 and MPK11 play a vital role in plant growth-to-defense transition.

CONCLUSIONS

Based on the dynamic network analysis of MeJA-induced plant resistance, we provide an important guideline for understanding the growth-to-defense transition of plants' response to environment stimuli. This study also provides a database with the key genes of plant defense induced by MeJA.

Nitric oxide coordinates growth, development, and stress response via histone modification and gene expression

Nitric oxide (NO) is a signaling molecule with multiple regulatory functions in plant physiology and stress response. In addition to direct effects on transcriptional machinery, NO executes its signaling function via epigenetic mechanisms. We report that light intensity-dependent changes in NO correspond to changes in global histone acetylation (H3, H3K9, and H3K9/K14) in Arabidopsis (Arabidopsis thaliana) wild-type leaves, and that this relationship depends on S-nitrosoglutathione reductase and histone deacetylase 6 (HDA6). The activity of HDA6 was sensitive to NO, demonstrating that NO participates in regulation of histone acetylation. Chromatin immunoprecipitation sequencing and RNA-seq analyses revealed that NO participates in the metabolic switch from growth and development to stress response. This coordinating function of NO might be particularly important in plant ability to adapt to a changing environment, and is therefore a promising foundation for mitigating the negative effects of climate change on plant productivity.

The sugar-responsive circadian clock regulator bZIP63 modulates plant growth

Adjustment to energy starvation is crucial to ensure growth and survival. In Arabidopsis thaliana (Arabidopsis), this process relies in part on the phosphorylation of the circadian clock regulator bZIP63 by SUCROSE non-fermenting RELATED KINASE1 (SnRK1), a key mediator of responses to low energy. We investigated the effects of mutations in bZIP63 on plant carbon (C) metabolism and growth. Results from phenotypic, transcriptomic and metabolomic analysis of bZIP63 mutants prompted us to investigate the starch accumulation pattern and the expression of genes involved in starch degradation and in the circadian oscillator. bZIP63 mutation impairs growth under light-dark cycles, but not under constant light. The reduced growth likely results from the accentuated C depletion towards the end of the night, which is caused by the accelerated starch degradation of bZIP63 mutants. The diel expression pattern of bZIP63 is dictated by both the circadian clock and energy levels, which could determine the changes in the circadian expression of clock and starch metabolic genes observed in bZIP63 mutants. We conclude that bZIP63 composes a regulatory interface between the metabolic and circadian control of starch breakdown to optimize C usage and plant growth.

Carbon/nitrogen metabolism and stress response networks - calcium-dependent protein kinases as the missing link?

Calcium-dependent protein kinases (CDPKs) play essential roles in plant development and stress responses. CDPKs have a conserved kinase domain, followed by an auto-inhibitory junction connected to the calmodulin-like domain that binds Ca2+. These structural features allow CDPKs to decode the dynamic changes in cytoplasmic Ca2+ concentrations triggered by hormones and by biotic and abiotic stresses. In response to these signals, CDPKs phosphorylate downstream protein targets to regulate growth and stress responses according to the environmental and developmental circumstances. The latest advances in our understanding of the metabolic, transcriptional, and protein-protein interaction networks involving CDPKs suggest that they have a direct influence on plant carbon/nitrogen (C/N) balance. In this review, we discuss how CDPKs could be key signaling nodes connecting stress responses with metabolic homeostasis, and acting together with the sugar and nutrient signaling hubs SnRK1, HXK1, and TOR to improve plant fitness.

Transcriptomic and metabolomic analyses of non-structural carbohydrates in red maple leaves

Plant sugars serve to balance nutrition, regulate development, and respond to biotic and abiotic stresses, whereas non-structural carbohydrates (NSCs) are essential energy sources that facilitate plant growth, metabolism, and environmental adaptation. To better elucidate the mechanisms of NSCs in red maple, ultrahigh-performance liquid chromatograph Q extractive mass spectrometry (UHPLC-QE-MS) and high-throughput RNA-sequencing were performed on green, red, and yellow leaves from a selected red maple mutant. In green leaves, the fructose phosphorylation process exhibited greater flux. In yellow leaves, sucrose and starch had a stronger capacity for synthesis and degradation, whereas in red leaves, there was a greater accumulation of trehalose and manninotriose. ArTPS5 positively regulated amylose, which was negatively regulated by ArFBP2, whereas ArFRK2 and ArFBP13 played a positive role in the biosynthesis of Sucrose-6P. Sucrose-6P also regulated anthocyanins and abscisic acid in red maple by affecting transcription factors. The results of this paper can assist with the control and optimization of the biosynthesis of NSCs in red maple, which may ultimately provide the foundation for influencing sugar production in Acer.

Mapping regulatory variants controlling gene expression in drought response and tolerance in maize

BACKGROUND

Gene expression is a key determinant of cellular response. Natural variation in gene expression bridges genetic variation to phenotypic alteration. Identification of the regulatory variants controlling the gene expression in response to drought, a major environmental threat of crop production worldwide, is of great value for drought-tolerant gene identification.

RESULTS

A total of 627 RNA-seq analyses are performed for 224 maize accessions which represent a wide genetic diversity under three water regimes; 73,573 eQTLs are detected for about 30,000 expressing genes with high-density genome-wide single nucleotide polymorphisms, reflecting a comprehensive and dynamic genetic architecture of gene expression in response to drought. The regulatory variants controlling the gene expression constitutively or drought-dynamically are unraveled. Focusing on dynamic regulatory variants resolved to genes encoding transcription factors, a drought-responsive network reflecting a hierarchy of transcription factors and their target genes is built. Moreover, 97 genes are prioritized to associate with drought tolerance due to their expression variations through the Mendelian randomization analysis. One of the candidate genes, Abscisic acid 8'-hydroxylase, is verified to play a negative role in plant drought tolerance.

CONCLUSIONS

This study unravels the effects of genetic variants on gene expression dynamics in drought response which allows us to better understand the role of distal and proximal genetic effects on gene expression and phenotypic plasticity. The prioritized drought-associated genes may serve as direct targets for functional investigation or allelic mining.

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

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

Putative cis-Regulatory Elements Predict Iron Deficiency Responses in Arabidopsis Roots

Plant iron deficiency (-Fe) activates a complex regulatory network that coordinates root Fe uptake and distribution to sink tissues. In Arabidopsis (Arabidopsis thaliana), FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT), a basic helix-loop-helix (bHLH) transcription factor (TF), regulates root Fe acquisition genes. Many other -Fe-induced genes are FIT independent, and instead regulated by other bHLH TFs and by yet unknown TFs. The cis-regulatory code, that is, the cis-regulatory elements (CREs) and their combinations that regulate plant -Fe-responses, remains largely elusive. Using Arabidopsis root transcriptome data and coexpression clustering, we identified over 100 putative CREs (pCREs) that predicted -Fe-induced gene expression in computational models. To assess pCRE properties and possible functions, we used large-scale in vitro TF binding data, positional bias, and evolutionary conservation. As one example, our approach uncovered pCREs resembling IDE1 (iron deficiency-responsive element 1), a known grass -Fe response CRE. Arabidopsis IDE1-likes were associated with FIT-dependent gene expression, more specifically with biosynthesis of Fe-chelating compounds. Thus, IDE1 seems to be conserved in grass and nongrass species. Our pCREs matched among others in vitro binding sites of B3, NAC, bZIP, and TCP TFs, which might be regulators of -Fe responses. Altogether, our findings provide a comprehensive source of cis-regulatory information for -Fe-responsive genes that advance our mechanistic understanding and inform future efforts in engineering plants with more efficient Fe uptake or transport systems.

Sugar Signaling and Post-transcriptional Regulation in Plants: An Overlooked or an Emerging Topic?

Plants are autotrophic organisms that self-produce sugars through photosynthesis. These sugars serve as an energy source, carbon skeletons, and signaling entities throughout plants' life. Post-transcriptional regulation of gene expression plays an important role in various sugar-related processes. In cells, it is regulated by many factors, such as RNA-binding proteins (RBPs), microRNAs, the spliceosome, etc. To date, most of the investigations into sugar-related gene expression have been focused on the transcriptional level in plants, while only a few studies have been conducted on post-transcriptional mechanisms. The present review provides an overview of the relationships between sugar and post-transcriptional regulation in plants. It addresses the relationships between sugar signaling and RBPs, microRNAs, and mRNA stability. These new items insights will help to reach a comprehensive understanding of the diversity of sugar signaling regulatory networks, and open onto new investigations into the relevance of these regulations for plant growth and development.

Arabidopsis thaliana Plants Engineered To Produce Astaxanthin Show Enhanced Oxidative Stress Tolerance and Bacterial Pathogen Resistance

Carotenoids play key roles in photosynthesis and photoprotection. Few multicellular plants produce the ketocarotenoid astaxanthin, a strong antioxidant; however, Arabidopsis thaliana lines overexpressing the Chlamydomonas reinhardtii β-carotene ketolase (CrBKT) accumulated high amounts of astaxanthin in the leaves. In this study, we investigated the changed regulation of key metabolic pathways and the tolerance of the engineered plants to biotic and abiotic stresses resulting from the heterologous expression of CrBKT. Transcriptome analysis identified 1633 and 1722 genes that were differentially expressed in the leaves and siliques, respectively, of CrBKT-overexpressing plants (line CR5) as compared to wild-type Arabidopsis. These genes were enriched in the carotenoid biosynthetic pathways, and plant hormone biosynthesis and signaling pathways. In particular, metabolic profiling showed that, as compared to the wild-type leaves and siliques, overexpression of CrBKT increased the levels of most amino acids, but decreased the contents of sugars and carbohydrates. Furthermore, CR5 plants had lower sensitivity to abscisic acid (ABA) and increased tolerance to oxidative stress. CR5 plants also exhibited enhanced resistance to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Our study provides insight into the regulation of carotenoids and the related pathways, which may be involved in plant response to oxidative stress and pathogen infection.

WRKY1 Mediates Transcriptional Regulation of Light and Nitrogen Signaling Pathways

Plant responses to multiple environmental stimuli must be integrated to enable them to adapt their metabolism and development. Light and nitrogen (N) are two such stimuli whose downstream signaling pathways must be intimately connected to each other to control plant energy status. Here, we describe the functional role of the WRKY1 transcription factor in controlling genome-wide transcriptional reprogramming of Arabidopsis (Arabidopsis thaliana) leaves in response to individual and combined light and N signals. This includes a cross-regulatory network consisting of 724 genes regulated by WRKY1 and involved in both N and light signaling pathways. The loss of WRKY1 gene function has marked effects on the light and N response of genes involved in N uptake and assimilation (primary metabolism) as well as stress response pathways (secondary metabolism). Our results at the transcriptome and at the metabolite analysis level support a model in which WRKY1 enables plants to activate genes involved in the recycling of cellular carbon resources when light is limiting but N is abundant and upregulate amino acid metabolism when both light and N are limiting. In this potential energy conservation mechanism, WRKY1 integrates information about cellular N and light energy resources to trigger changes in plant metabolism.

Arabidopsis GSM1 is involved in ABI4-regulated ABA signaling under high-glucose condition in early seedling growth

In plants, sugar acts as an essential signaling molecule that modulates various aspects of metabolism, growth and development, which are also controlled by phytohormones. However, the molecular mechanism of cross-talk between sugar and phytohormones still remains to be elucidated. We have identified gsm1 (glucose-hypersensitive mutant 1) as a mutant with impaired cotyledon development that shows sensitivity to exogenous abscisic acid (ABA). The addition of fluridone can reverse the glucose (Glc) inhibitory effect in gsm1, implying that endogenous ABA is involved in the Glc response of gsm1. In 4.5% Glc, the expression of Glc-induced ABA-responsive genes in gsm1-1 was nearly two times higher than that in the wild type. Compared to gsm1-1, the gsm1-1 abi4-1 double mutant exhibited reduced sensitivity to Glc and ABA, which was similar to the Glc and ABA insensitive phenotype of abi4-1, suggesting that ABI4 is epistatic to GSM1. In the treatment with 4.5% Glc, the GSM1 transcript level was greatly increased in abi4-1 by almost 4-fold of that in the wild type. These data suggest that GSM1 plays an important role in the ABI4-regulated Glc-ABA signaling cascade during Arabidopsis early seedling growth.

WRKY18 and WRKY53 Coordinate with HISTONE ACETYLTRANSFERASE1 to Regulate Rapid Responses to Sugar

Sugars provide a source of energy; they also function as signaling molecules that regulate gene expression, affect metabolism, and alter growth in plants. Rapid responses to sugar signaling and metabolism are essential for optimal growth and fitness, but the regulatory mechanisms underlying these are largely unknown. In this study, we found that the rapid induction of sugar responses in Arabidopsis (Arabidopsis thaliana) requires the W-box cis-elements in the promoter region of GLC 6-PHOSPHATE/PHOSPHATE TRANSLOCATOR2, a well-studied sugar response marker gene. The transcription factors WRKY18 and WRKY53 directly bind to the W-Box cis-elements in the promoter region of sugar response genes and activate their expression. In addition, HISTONE ACETYLTRANSFERASE 1 (HAC1) is recruited to the WRKY18 and WRKY53 complex that resides on the promoters. In this complex, HAC1 facilitates the acetylation of histone 3 Lys 27 (H3K27ac) on the sugar-responsive genes. Taken together, our findings demonstrate a mechanism by which sugar regulates chromatin modification and gene expression, thus helping plants to adjust their growth in response to environmental changes.

A stress-responsive bZIP transcription factor OsbZIP62 improves drought and oxidative tolerance in rice

BACKGROUND

Drought is a major abiotic stress factor that influences the yield of crops. Basic leucine zipper motif (bZIP) transcription factors play an important regulatory role in plant drought stress responses. However, the functions of a number of bZIP transcription factors in rice are still unknown.

RESULTS

In this study, a novel drought stress-related bZIP transcription factor, OsbZIP62, was identified in rice. This gene was selected from a transcriptome analysis of several typical rice varieties with different drought tolerances. OsbZIP62 expression was induced by drought, hydrogen peroxide, and abscisic acid (ABA) treatment. Overexpression of OsbZIP62-VP64 (OsbZIP62V) enhanced the drought tolerance and oxidative stress tolerance of transgenic rice, while osbzip62 mutants exhibited the opposite phenotype. OsbZIP62-GFP was localized to the nucleus, and the N-terminal sequence (amino acids 1-68) was necessary for the transcriptional activation activity of OsbZIP62. RNA-seq analysis showed that the expression of many stress-related genes (e.g., OsGL1, OsNAC10, and DSM2) was upregulated in OsbZIP62V plants. Moreover, OsbZIP62 could bind to the promoters of several putative target genes and could interact with stress/ABA-activated protein kinases (SAPKs).

CONCLUSIONS

OsbZIP62 is involved in ABA signalling pathways and positively regulates rice drought tolerance by regulating the expression of genes associated with stress, and this gene could be used for the genetic modification of crops with improved drought tolerance.

RNA-Seq and iTRAQ reveal multiple pathways involved in storage root formation and development in sweet potato (Ipomoea batatas L.)

BACKGROUND

Sweet potato (Ipomoea batatas L.) is the sixth most important food crop in the world. The formation and development of storage roots in sweet potato is a highly complicated and genetically programmed process. However, the underlying mechanisms of storage root development have not yet been elucidated.

RESULTS

To better understand the molecular mechanisms involved in storage root development, a combined analysis of the transcriptome and proteome of sweet potato fibrous roots (F) and storage roots at four different stages (D1, D3, D5 and D10) was performed in the present study. A total of 26,273 differentially expressed genes were identified in a comparison between the fibrous root library and four storage root libraries, while 2558 proteins showed a 1.0-fold or greater expression difference as indicated by isobaric tags for relative and absolute quantitation (iTRAQ) analysis. The combination of the transcriptome and proteome analyses and morphological and physiological data revealed several critical pathways involved in storage root formation and development. First, genes/proteins involved in the development of meristems/cambia and starch biosynthesis were all significantly upregulated in storage roots compared with fibrous roots. Second, multiple phytohormones and the genes related to their biosynthesis showed differential expression between fibrous roots and storage roots. Third, a large number of transcription factors were differentially expressed during storage root initiation and development, which suggests the importance of transcription factor regulation in the development of storage roots. Fourth, inconsistent gene expression was found between the transcriptome and proteome data, which indicated posttranscriptional regulatory activity during the development of storage roots.

CONCLUSION

Overall, these results reveal multiple events associated with storage root development and provide new insights into the molecular mechanisms underlying the regulatory networks involved in storage root development.

Gene regulatory networks for lignin biosynthesis in switchgrass (Panicum virgatum)

Cell wall recalcitrance is the major challenge to improving saccharification efficiency in converting lignocellulose into biofuels. However, information regarding the transcriptional regulation of secondary cell wall biogenesis remains poor in switchgrass (Panicum virgatum), which has been selected as a biofuel crop in the United States. In this study, we present a combination of computational and experimental approaches to develop gene regulatory networks for lignin formation in switchgrass. To screen transcription factors (TFs) involved in lignin biosynthesis, we developed a modified method to perform co-expression network analysis using 14 lignin biosynthesis genes as bait (target) genes. The switchgrass lignin co-expression network was further extended by adding 14 TFs identified in this study, and seven TFs identified in previous studies, as bait genes. Six TFs (PvMYB58/63, PvMYB42/85, PvMYB4, PvWRKY12, PvSND2 and PvSWN2) were targeted to generate overexpressing and/or down-regulated transgenic switchgrass lines. The alteration of lignin content, cell wall composition and/or plant growth in the transgenic plants supported the role of the TFs in controlling secondary wall formation. RNA-seq analysis of four of the transgenic switchgrass lines revealed downstream target genes of the secondary wall-related TFs and crosstalk with other biological pathways. In vitro transactivation assays further confirmed the regulation of specific lignin pathway genes by four of the TFs. Our meta-analysis provides a hierarchical network of TFs and their potential target genes for future manipulation of secondary cell wall formation for lignin modification in switchgrass.

The Sugar-Signaling Hub: Overview of Regulators and Interaction with the Hormonal and Metabolic Network

Plant growth and development has to be continuously adjusted to the available resources. Their optimization requires the integration of signals conveying the plant metabolic status, its hormonal balance, and its developmental stage. Many investigations have recently been conducted to provide insights into sugar signaling and its interplay with hormones and nitrogen in the fine-tuning of plant growth, development, and survival. The present review emphasizes the diversity of sugar signaling integrators, the main molecular and biochemical mechanisms related to the sugar-signaling dependent regulations, and to the regulatory hubs acting in the interplay of the sugar-hormone and sugar-nitrogen networks. It also contributes to compiling evidence likely to fill a few knowledge gaps, and raises new questions for the future.

The Sugar-Signaling Hub: Overview of Regulators and Interaction with the Hormonal and Metabolic Network

Plant growth and development has to be continuously adjusted to the available resources. Their optimization requires the integration of signals conveying the plant metabolic status, its hormonal balance, and its developmental stage. Many investigations have recently been conducted to provide insights into sugar signaling and its interplay with hormones and nitrogen in the fine-tuning of plant growth, development, and survival. The present review emphasizes the diversity of sugar signaling integrators, the main molecular and biochemical mechanisms related to the sugar-signaling dependent regulations, and to the regulatory hubs acting in the interplay of the sugar-hormone and sugar-nitrogen networks. It also contributes to compiling evidence likely to fill a few knowledge gaps, and raises new questions for the future.

Circadian Entrainment in Arabidopsis by the Sugar-Responsive Transcription Factor bZIP63

Synchronization of circadian clocks to the day-night cycle ensures the correct timing of biological events. This entrainment process is essential to ensure that the phase of the circadian oscillator is synchronized with daily events within the environment [1], to permit accurate anticipation of environmental changes [2, 3]. Entrainment in plants requires phase changes in the circadian oscillator, through unidentified pathways, which alter circadian oscillator gene expression in response to light, temperature, and sugars [4, 5, 6]. To determine how circadian clocks respond to metabolic rhythms, we investigated the mechanisms by which sugars adjust the circadian phase in Arabidopsis [5]. We focused upon metabolic regulation because interactions occur between circadian oscillators and metabolism in several experimental systems [5, 7, 8, 9], but the molecular mechanisms are unidentified. Here, we demonstrate that the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) regulates the circadian oscillator gene PSEUDO RESPONSE REGULATOR7 (PRR7) to change the circadian phase in response to sugars. We find that SnRK1, a sugar-sensing kinase that regulates bZIP63 activity and circadian period [10, 11, 12, 13, 14] is required for sucrose-induced changes in circadian phase. Furthermore, TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1), which synthesizes the signaling sugar trehalose-6-phosphate, is required for circadian phase adjustment in response to sucrose. We demonstrate that daily rhythms of energy availability can entrain the circadian oscillator through the function of bZIP63, TPS1, and the KIN10 subunit of the SnRK1 energy sensor. This identifies a molecular mechanism that adjusts the circadian phase in response to sugars.

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The transcription factor bZIP63 binds and regulates the circadian clock gene PRR7

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bZIP63 is required for adjustment of circadian period by sugars

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Trehalose-6-phosphate metabolism and KIN10 signaling regulate circadian period

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Sugar signals establish the correct circadian phase in light and dark cycles

Sugar-responsive transcription factor bZIP3 affects leaf shape in Arabidopsis plants

Sugars are essential for plant metabolism, growth and development. Plants must therefore manage their growth and developmental processes in response to sugar availability. Sugar signaling pathways constitute a complicated molecular network and are associated with global transcriptional regulation. However, the molecular mechanisms underlying sugar signaling remain largely unclear. This study reports that the protein basic-region leucine zipper 3 (bZIP3) is a novel sugar-responsive transcription factor in Arabidopsis plants. The expression of bZIP3 was rapidly repressed by sugar. Genetic analysis indicated that bZIP3 expression was modulated by the SNF1-RELATED KINASE 1 (SnRK1) pathway. Moreover, transgenic plants overexpressing bZIP3 and dominant repressor form bZIP3-SRDX showed aberrant shaped cotyledons with hyponastic bending. These findings suggest that bZIP3 plays a role in plant responses to sugars and is also associated with leaf development.

The C/S1 bZIP Network: A Regulatory Hub Orchestrating Plant Energy Homeostasis

Sustaining energy homeostasis is crucial to every living being. To balance energy supply and demand, plants make use of an evolutionarily conserved management system consisting of two counteracting kinases, TOR (TARGET OF RAPAMYCIN) and SnRK1 (Snf1-RELATED PROTEIN KINASE 1). SnRK1 is involved in reorganizing enzymatic and transcriptional responses to survive energy-limiting conditions. Recently, members of the bZIP (basic leucine zipper) transcription factor family have been established as SnRK1 downstream mediators. We review here current knowledge on the functional impact of these group C and S₁ bZIPs, and analyze their regulation by environmental and endogenous cues. Given their specific homo- and heterodimerization, the so-called C/S₁ bZIP network is proposed to act as a signaling hub that coordinates plant development and stress responses.

Transcript Profiling Identifies NAC-Domain Genes Involved in Regulating Wall Ingrowth Deposition in Phloem Parenchyma Transfer Cells of Arabidopsis thaliana

Transfer cells (TCs) play important roles in facilitating enhanced rates of nutrient transport at key apoplasmic/symplasmic junctions along the nutrient acquisition and transport pathways in plants. TCs achieve this capacity by developing elaborate wall ingrowth networks which serve to increase plasma membrane surface area thus increasing the cell's surface area-to-volume ratio to achieve increased flux of nutrients across the plasma membrane. Phloem parenchyma (PP) cells of Arabidopsis leaf veins trans-differentiate to become PP TCs which likely function in a two-step phloem loading mechanism by facilitating unloading of photoassimilates into the apoplasm for subsequent energy-dependent uptake into the sieve element/companion cell (SE/CC) complex. We are using PP TCs in Arabidopsis as a genetic model to identify transcription factors involved in coordinating deposition of the wall ingrowth network. Confocal imaging of pseudo-Schiff propidium iodide-stained tissue revealed different profiles of temporal development of wall ingrowth deposition across maturing cotyledons and juvenile leaves, and a basipetal gradient of deposition across mature adult leaves. RNA-Seq analysis was undertaken to identify differentially expressed genes common to these three different profiles of wall ingrowth deposition. This analysis identified 68 transcription factors up-regulated two-fold or more in at least two of the three experimental comparisons, with six of these transcription factors belonging to Clade III of the NAC-domain family. Phenotypic analysis of these NAC genes using insertional mutants revealed significant reductions in levels of wall ingrowth deposition, particularly in a double mutant of NAC056 and NAC018, as well as compromised sucrose-dependent root growth, indicating impaired capacity for phloem loading. Collectively, these results support the proposition that Clade III members of the NAC-domain family in Arabidopsis play important roles in regulating wall ingrowth deposition in PP TCs.

Overexpression of a wheat (Triticum aestivum L.) bZIP transcription factor gene, TabZIP6, decreased the freezing tolerance of transgenic Arabidopsis seedlings by down-regulating the expression of CBFs

The basic leucine zipper (bZIP) proteins play important roles against abiotic stress in plants, including cold stress. However, most bZIPs involved in plant freezing tolerance are positive regulators. Only a few bZIPs function negatively in cold stress response. In this study, TabZIP6, a Group C bZIP transcription factor gene from common wheat (Triticum aestivum L.), was cloned and characterized. The transcript of TabZIP6 was strongly induced by cold treatment (4 °C). TabZIP6 is a nuclear-localized protein with transcriptional activation activity. Arabidopsis plants overexpressing TabZIP6 showed decreased tolerance to freezing stress. Microarray as well as quantitative real-time PCR (qRT-PCR) analysis showed that CBFs and some key COR genes, including COR47 and COR15B, were down-regulated by cold treatment in TabZIP6-overexpressing Arabidopsis lines. TabZIP6 was capable of binding to the G-box motif and the CBF1 and CBF3 promoters in yeast cells. A yeast two-hybrid assay revealed that TabZIP6, as well as the other two Group S bZIP proteins involved in cold stress tolerance in wheat, Wlip19 and TaOBF1, can form homodimers by themselves and heterodimers with each other. These results suggest that TabZIP6 may function negatively in the cold stress response by binding to the promoters of CBFs, and thereby decreasing the expression of downstream COR genes in TabZIP6-overexpressing Arabidopsis seedlings.

Construction of a network describing asparagine metabolism in plants and its application to the identification of genes affecting asparagine metabolism in wheat under drought and nutritional stress

A detailed network describing asparagine metabolism in plants was constructed using published data from Arabidopsis (Arabidopsis thaliana) maize (Zea mays), wheat (Triticum aestivum), pea (Pisum sativum), soybean (Glycine max), lupin (Lupus albus), and other species, including animals. Asparagine synthesis and degradation is a major part of amino acid and nitrogen metabolism in plants. The complexity of its metabolism, including limiting and regulatory factors, was represented in a logical sequence in a pathway diagram built using yED graph editor software. The network was used with a Unique Network Identification Pipeline in the analysis of data from 18 publicly available transcriptomic data studies. This identified links between genes involved in asparagine metabolism in wheat roots under drought stress, wheat leaves under drought stress, and wheat leaves under conditions of sulfur and nitrogen deficiency. The network represents a powerful aid for interpreting the interactions not only between the genes in the pathway but also among enzymes, metabolites and smaller molecules. It provides a concise, clear understanding of the complexity of asparagine metabolism that could aid the interpretation of data relating to wider amino acid metabolism and other metabolic processes.

Evolutionary and expression analyses of soybean basic Leucine zipper transcription factor family

BACKGROUND

Soybean, a major legume crop native to East Asia, presents a wealth of resources for utilization. The basic leucine zipper (bZIP) transcription factors play important roles in various biological processes including developmental regulation and responses to environmental stress stimuli. Currently, little information is available regarding the bZIP family in the legume crop soybean.

RESULTS

Using a genome-wide domain analysis, we identified 160 GmbZIP genes in soybean genome, named from GmbZIP1 to GmbZIP160. These 160GmbZIP genes, distributed unevenly across 20 chromosomes, were grouped into 12 subfamilies based on phylogenetic analysis. Gene structure and conserved motif analyses showed that GmbZIP within the same subfamily shared similar intron-exon organizations and motif composition. Syntenic and phylogenetic analyses identified 40 Arabidopsis bZIP genes and 83 soybean bZIP genes as orthologs. By investigating the expression profiling of GmbZIP in different tissues and under drought and flooding stresses, we showed that a majority of GmbZIP (83.44%) exhibited transcript abundance in all examined tissues and 75.6% displayed transcript changes after drought and flooding treatment, suggesting that GmbZIP may play a broad role in soybean development and response to water stress.

CONCLUSIONS

One hundred sixty GmbZIP genes were identified in soybean genome. Our results provide insights for the evolutionary history of bZIP family in soybean and shed light on future studies on the function of bZIP genes in response to water stress in soybean.

The Energy-Signaling Hub SnRK1 Is Important for Sucrose-Induced Hypocotyl Elongation

Emerging seedlings respond to environmental conditions such as light and temperature to optimize their establishment. Seedlings grow initially through elongation of the hypocotyl, which is regulated by signaling pathways that integrate environmental information to regulate seedling development. The hypocotyls of Arabidopsis (Arabidopsis thaliana) also elongate in response to sucrose. Here, we investigated the role of cellular sugar-sensing mechanisms in the elongation of hypocotyls in response to Suc. We focused upon the role of SnRK1, which is a sugar-signaling hub that regulates metabolism and transcription in response to cellular energy status. We also investigated the role of TPS1, which synthesizes the signaling sugar trehalose-6-P that is proposed to regulate SnRK1 activity. Under light/dark cycles, we found that Suc-induced hypocotyl elongation did not occur in tps1 mutants and overexpressors of KIN10 (AKIN10/SnRK1.1), a catalytic subunit of SnRK1. We demonstrate that the magnitude of Suc-induced hypocotyl elongation depends on the day length and light intensity. We identified roles for auxin and gibberellin signaling in Suc-induced hypocotyl elongation under short photoperiods. We found that Suc-induced hypocotyl elongation under light/dark cycles does not involve another proposed sugar sensor, HEXOKINASE1, or the circadian oscillator. Our study identifies novel roles for KIN10 and TPS1 in mediating a signal that underlies Suc-induced hypocotyl elongation in light/dark cycles.

Seasonal below-ground metabolism in switchgrass

Switchgrass (Panicum virgatum), a perennial, polyploid, C4 warm-season grass is among the foremost herbaceous species being advanced as a source of biomass for biofuel end uses. At the end of every growing season, the aerial tissues senesce, and the below-ground rhizomes become dormant. Future growth is dependent on the successful over-wintering of the rhizomes. Although the importance of rhizome health to overall year-upon-year plant productivity has been long recognized, there is limited information on seasonal changes occurring during dormancy at both the transcriptome and metabolite levels. Here, global changes in transcriptomes and metabolites were investigated over two growing seasons in rhizomes harvested from field-grown plants. The objectives were: (a) synthesize information on cellular processes that lead to dormancy; and (b) provide models that could account for major metabolic pathways present in dormant switchgrass rhizomes. Overall, metabolism during dormancy appeared to involve discrete but interrelated events. One was a response to abscisic acid that resulted in dehydration, increases in osmolytes and upregulation of autophagic processes, likely through the target of rapamycin complex and sucrose non-fermentative-related kinase-based signaling cascades. Another was a recalibration of energy transduction through apparent reductions in mitochondrial oxidative phosphorylation, increases in substrate level generation of ATP and reducing equivalents, and recycling of N and possibly CO₂ through refixation. Lastly, transcript abundances indicated that cold-related signaling was also occurring. Altogether, these data provide a detailed overview of rhizome metabolism, especially during dormancy, which can be exploited in the future to improve winter survival in switchgrass.

Evidence for a Strong Correlation Between Transcription Factor Protein Disorder and Organismic Complexity

Studies of diverse phylogenetic lineages reveal that protein disorder increases in concert with organismic complexity but that differences nevertheless exist among lineages. To gain insight into this phenomenology, we analyzed all of the transcription factor (TF) families for which sequences are known for 17 species spanning bacteria, yeast, algae, land plants, and animals and for which the number of different cell types has been reported in the primary literature. Although the fraction of disordered residues in TF sequences is often moderately or poorly correlated with organismic complexity as gauged by cell-type number (r² < 0.5), an unbiased and phylogenetically broad analysis shows that organismic complexity is positively and strongly correlated with the total number of TFs, the number of their spliced variants and their total disordered residues content (r² > 0.8). Furthermore, the correlation between the fraction of disordered residues and cell-type number becomes stronger when confined to the TF families participating in cell cycle, cell size, cell division, cell differentiation, or cell proliferation, and other important developmental processes. The data also indicate that evolutionarily simpler organisms allow for the detection of subtle differences in the conserved IDRs of TFs as well as changes in variable IDRs, which can influence the DNA recognition and multifunctionality of TFs through direct or indirect mechanisms. Although strong correlations cannot be taken as evidence for cause-and-effect relationships, we interpret our data to indicate that increasing TF disorder likely was an important factor contributing to the evolution of organismic complexity and not merely a concurrent unrelated effect of increasing organismic complexity.

Predictive Models of Spatial Transcriptional Response to High Salinity

Plants are exposed to a variety of environmental conditions, and their ability to respond to environmental variation depends on the proper regulation of gene expression in an organ-, tissue-, and cell type-specific manner. Although our knowledge of how stress responses are regulated is accumulating, a genome-wide model of how plant transcription factors (TFs) and cis-regulatory elements control spatially specific stress response has yet to emerge. Using Arabidopsis (Arabidopsis thaliana) as a model, we identified a set of 1,894 putative cis-regulatory elements (pCREs) that are associated with high-salinity (salt) up-regulated genes in the root or the shoot. We used these pCREs to develop computational models that can better predict salt up-regulated genes in the root and shoot compared with models based on known TF binding motifs. In addition, we incorporated TF binding sites identified via large-scale in vitro assays, chromatin accessibility, evolutionary conservation, and pCRE combinatorial relationships in machine learning models and found that only consideration of pCRE combinations led to better performance in salt up-regulation prediction in the root and shoot. Our results suggest that the plant organ transcriptional response to high salinity is regulated by a core set of pCREs and provide a genome-wide view of the cis-regulatory code of plant spatial transcriptional responses to environmental stress.

Identification of a novel bZIP transcription factor in Camellia sinensis as a negative regulator of freezing tolerance in transgenic arabidopsis

BACKGROUND AND AIMS

Basic region/leucine zipper (bZIP) transcription factors play vital roles in the abiotic stress response of plants. However, little is known about the function of bZIP genes in Camellia sinensis .

METHODS

CsbZIP6 was overexpressed in Arabidopsis thaliana . Effects of CsbZIP6 overexpression on abscisic acid (ABA) sensitivity, freezing tolerance and the expression of cold-responsive genes in arabidopsis were studied.

KEY RESULTS

CsbZIP6 was induced during cold acclimation in tea plant. Constitutive overexpression of CsbZIP6 in arabidopsis lowered the plants' tolerance to freezing stress and ABA exposure during seedling growth. Compared with wild-type (WT) plants, CsbZIP6 overexpression (OE) lines exhibited increased levels of electrolyte leakage (EL) and malondialdehyde (MDA) contents, and reduced levels of total soluble sugars (TSS) under cold stress conditions. Microarray analysis of transgenic arabidopsis revealed that many differentially expressed genes (DEGs) between OE lines and WT plants could be mapped to 'response to cold' and 'response to water deprivation' terms based on Gene Ontology analysis. Interestingly, CsbZIP6 overexpression repressed most of the cold- and drought-responsive genes as well as starch metabolism under cold stress conditions.

CONCLUSIONS

The data suggest that CsbZIP6 functions as a negative regulator of the cold stress response in A. thaliana , potentially by down-regulating cold-responsive genes.

A Novel Wheat C-bZIP Gene, TabZIP14-B, Participates in Salt and Freezing Tolerance in Transgenic Plants

The group C-bZIP transcription factors (TFs) are involved in diverse biological processes, such as the regulation of seed storage protein (SSP) production and the responses to pathogen challenge and abiotic stress. However, our knowledge of the abiotic functions of group C-bZIP genes in wheat remains limited. Here, we present the function of a novel TabZIP14-B gene in wheat. This gene belongs to the group C-bZIP TFs and contains six exons and five introns; three haplotypes were identified among accessions of tetraploid and hexaploid wheat. A subcellular localization analysis indicated that TabZIP14-B was targeted to the nucleus of tobacco epidermal cells. A transactivation assay demonstrated that TabZIP14-B showed transcriptional activation ability and was capable of binding the abscisic acid (ABA) responsive element (ABRE) in yeast. RT-qPCR revealed that TabZIP14-B was expressed in the roots, stems, leaves, and young spikes and was up-regulated by exogenous ABA, salt, low-temperature, and polyethylene glycol (PEG) stress treatments. Furthermore, Arabidopsis plants overexpressing TabZIP14-B exhibited enhanced tolerance to salt, freezing stresses and ABA sensitivity. Overexpression of TabZIP14-B resulted in increased expression of the AtRD29A, AtCOR47, AtRD20, AtGSTF6, and AtRAB18 genes and changes in several physiological characteristics. These results suggest that TabZIP14-B could function as a positive regulator in mediating the abiotic stress response.

The plant energy sensor: evolutionary conservation and divergence of SnRK1 structure, regulation, and function

The SnRK1 (SNF1-related kinase 1) kinases are the plant cellular fuel gauges, activated in response to energy-depleting stress conditions to maintain energy homeostasis while also gatekeeping important developmental transitions for optimal growth and survival. Similar to their opisthokont counterparts (animal AMP-activated kinase, AMPK, and yeast Sucrose Non-Fermenting 1, SNF), they function as heterotrimeric complexes with a catalytic (kinase) α subunit and regulatory β and γ subunits. Although the overall configuration of the kinase complexes is well conserved, plant-specific structural modifications (including a unique hybrid βγ subunit) and associated differences in regulation reflect evolutionary divergence in response to fundamentally different lifestyles. While AMP is the key metabolic signal activating AMPK in animals, the plant kinases appear to be allosterically inhibited by sugar-phosphates. Their function is further fine-tuned by differential subunit expression, localization, and diverse post-translational modifications. The SnRK1 kinases act by direct phosphorylation of key metabolic enzymes and regulatory proteins, extensive transcriptional regulation (e.g. through bZIP transcription factors), and down-regulation of TOR (target of rapamycin) kinase signaling. Significant progress has been made in recent years. New tools and more directed approaches will help answer important fundamental questions regarding their structure, regulation, and function, as well as explore their potential as targets for selection and modification for improved plant performance in a changing environment.

A Glycine soja methionine sulfoxide reductase B5a interacts with the Ca(2+) /CAM-binding kinase GsCBRLK and activates ROS signaling under carbonate alkaline stress

Although research has extensively illustrated the molecular basis of plant responses to salt and high-pH stresses, knowledge on carbonate alkaline stress is poor and the specific responsive mechanism remains elusive. We have previously characterized a Glycine soja Ca(2+) /CAM-dependent kinase GsCBRLK that could increase salt tolerance. Here, we characterize a methionine sulfoxide reductase (MSR) B protein GsMSRB5a as a GsCBRLK interactor by using Y2H and BiFc assays. Further analyses showed that the N-terminal variable domain of GsCBRLK contributed to the GsMSRB5a interaction. Y2H assays also revealed the interaction specificity of GsCBRLK with the wild soybean MSRB subfamily proteins, and determined that the BoxI/BoxII-containing regions within GsMSRBs were responsible for their interaction. Furthermore, we also illustrated that the N-terminal basic regions in GsMSRBs functioned as transit peptides, which targeted themselves into chloroplasts and thereby prevented their interaction with GsCBRLK. Nevertheless, deletion of these regions allowed them to localize on the plasma membrane (PM) and interact with GsCBRLK. In addition, we also showed that GsMSRB5a and GsCBRLK displayed overlapping tissue expression specificity and coincident expression patterns under carbonate alkaline stress. Phenotypic experiments demonstrated that GsMSRB5a and GsCBRLK overexpression in Arabidopsis enhanced carbonate alkaline stress tolerance. Further investigations elucidated that GsMSRB5a and GsCBRLK inhibited reactive oxygen species (ROS) accumulation by modifying the expression of ROS signaling, biosynthesis and scavenging genes. Summarily, our results demonstrated that GsCBRLK and GsMSRB5a interacted with each other, and activated ROS signaling under carbonate alkaline stress.

Genome-Wide Identification and Characterization of bZIP Transcription Factors in Brassica oleracea under Cold Stress

Cabbages (Brassica oleracea L.) are an important vegetable crop around world, and cold temperature is among the most significant abiotic stresses causing agricultural losses, especially in cabbage crops. Plant bZIP transcription factors play diverse roles in biotic/abiotic stress responses. In this study, 119 putative BolbZIP transcription factors were identified using amino acid sequences from several bZIP domain consensus sequences. The BolbZIP members were classified into 63 categories based on amino acid sequence similarity and were also compared with BrbZIP and AtbZIP transcription factors. Based on this BolbZIP identification and classification, cold stress-responsive BolbZIP genes were screened in inbred lines, BN106 and BN107, using RNA sequencing data and qRT-PCR. The expression level of the 3 genes, Bol008071, Bol033132, and Bol042729, was significantly increased in BN107 under cold conditions and was unchanged in BN106. The upregulation of these genes in BN107, a cold-susceptible inbred line, suggests that they might be significant components in the cold response. Among three identified genes, Bol033132 has 97% sequence similarity to Bra020735, which was identified in a screen for cold-related genes in B. rapa and a protein containing N-rich regions in LCRs. The results obtained in this study provide valuable information for understanding the potential function of BolbZIP transcription factors in cold stress responses.