A zinc finger protein RHL41 mediates the light acclimatization response in Arabidopsis

Zat12 Gene Ameliorates Temperature Stress in Wheat Transgenics by Modulating the Antioxidant Defense System

The present study was undertaken with the objective to reconnoiter the role of Zat12-related biochemical activities in temperature stress tolerance in wheat transgenic lines Z-8-12 1A, Z-8-12 1B, Z-8-19, and Z-15-10, which were produced by transforming wheat-cultivar PBW 621. Zat12 transgenics (ZT) along with non-transgenic (NT) wheat cultivars (PBW 621, PBW, 550, and HD 3086) were assessed at the three-weeks seedling stage under chilling (−2 °C and −4 °C) and heat (30 °C and 32 °C) stress. Specific activities of superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX), glutathione-S-transferase (GST), glutathione reductase (GR), and antioxidants (proline and ascorbate) were profoundly increased under temperature stress in ZT related to NT. However, under −4 °C and 32 °C, a significantly higher increase was reported. In contrast, H2O2 and MDA were found to be much lower in ZT than in NT. Similarly, lesser decreases in length, fresh weight, and dry weight of seedlings were reported in ZT at 30 °C and 32 °C. RT-PCR studies revealed the enhanced expression of Zat12 in the roots of seedlings at the 5, 10, and 14 days after germination (DAG) stages in ZT under the stress conditions. Upregulation of the antioxidant defense system in ZT and their better tolerance depict an alternative for wheat cultivation under temperature stress-prone areas.

The intertwining of Zn-finger motifs and abiotic stress tolerance in plants: Current status and future prospects

Environmental stresses such as drought, high salinity, and low temperature can adversely modulate the field crop's ability by altering the morphological, physiological, and biochemical processes of the plants. It is estimated that about 50% + of the productivity of several crops is limited due to various types of abiotic stresses either presence alone or in combination (s). However, there are two ways plants can survive against these abiotic stresses; a) through management practices and b) through adaptive mechanisms to tolerate plants. These adaptive mechanisms of tolerant plants are mostly linked to their signalling transduction pathway, triggering the action of plant transcription factors and controlling the expression of various stress-regulated genes. In recent times, several studies found that Zn-finger motifs have a significant function during abiotic stress response in plants. In the first report, a wide range of Zn-binding motifs has been recognized and termed Zn-fingers. Since the zinc finger motifs regulate the function of stress-responsive genes. The Zn-finger was first reported as a repeated Zn-binding motif, comprising conserved cysteine (Cys) and histidine (His) ligands, in Xenopus laevis oocytes as a transcription factor (TF) IIIA (or TFIIIA). In the proteins where Zn²⁺ is mainly attached to amino acid residues and thus espousing a tetrahedral coordination geometry. The physical nature of Zn-proteins, defining the attraction of Zn-proteins for Zn²⁺, is crucial for having an in-depth knowledge of how a Zn²⁺ facilitates their characteristic function and how proteins control its mobility (intra and intercellular) as well as cellular availability. The current review summarized the concept, importance and mechanisms of Zn-finger motifs during abiotic stress response in plants.

Genome-Wide Identification of Strawberry C2H2-ZFP C1-2i Subclass and the Potential Function of FaZAT10 in Abiotic Stress

C2H2-type zinc finger proteins (C2H2-ZFPs) play a key role in various plant biological processes and responses to environmental stresses. In Arabidopsisthaliana, C2H2-ZFP members with two zinc finger domains have been well-characterized in response to abiotic stresses. To date, the functions of these genes in strawberries are still uncharacterized. Here, 126 C2H2-ZFPs in cultivated strawberry were firstly identified using the recently sequenced Fragaria × ananassa genome. Among these C2H2-ZFPs, 46 members containing two zinc finger domains in cultivated strawberry were further identified as the C1-2i subclass. These genes were unevenly distributed on 21 chromosomes and classified into five groups according to the phylogenetic relationship, with similar physicochemical properties and motif compositions in the same group. Analyses of conserved domains and gene structures indicated the evolutionary conservation of the C1-2i subclass. A Ka/Ks analysis indicated that the C1-2i members were subjected to purifying selection during evolution. Furthermore, FaZAT10, a typical C2H2-ZFP, was isolated. FaZAT10 was expressed the highest in roots, and it was induced by drought, salt, low-temperature, ABA, and MeJA treatments. It was localized in the nucleus and showed no transactivation activity in yeast cells. Overall, these results provide useful information for enriching the analysis of the ZFPs gene family in strawberry, and they provide support for revealing the mechanism of FaZAT10 in the regulatory network of abiotic stress.

Effects of exogenous calcium on the drought response of the tea plant (Camellia sinensis (L.) Kuntze)

Background

Drought is one of the major factors reducing the yield of many crops worldwide, including the tea crop (Camellia sinensis (L.) Kuntze). Calcium participates in most of cellular signaling processes, and its important role in stress detection and triggering a response has been shown in many crops. The aim of this study was to evaluate possible effects of calcium on the tea plant response to drought.

Methods

Experiments were conducted using 3-year-old potted tea plants of the best local cultivar Kolkhida. Application of ammonium nitrate (control treatment) or calcium nitrate (Ca treatment) to the soil was performed before drought induction. Next, a 7-day drought was induced in both groups of plants. The following physiological parameters were measured: relative electrical conductivity, pH of cell sap, and concentrations of cations, sugars, and amino acids. In addition, relative expression levels of 40 stress-related and crop quality-related genes were analyzed.

Results

Under drought stress, leaf electrolyte leakage differed significantly, indicating greater damage to cell membranes in control plants than in Ca-treated plants. Calcium application resulted in greater pH of cell sap; higher accumulation of tyrosine, methionine, and valine; and a greater Mg²⁺ content as compared to control plants. Drought stress downregulated most of the quality-related genes in both groups of tea plants. By contrast, significant upregulation of some genes was observed, namely CRK45, NAC26, TPS11, LOX1, LOX6, Hydrolase22, DREB26, SWEET2, GS, ADC, DHN2, GOLS1, GOLS3, and RHL41. Among them, three genes (LOX1, RHL41, and GOLS1) showed 2-3 times greater expression in Ca-treated plants than in control plants. Based on these results, it can be speculated that calcium affects galactinol biosynthesis and participates in the regulation of stomatal aperture not only through activation of abscisic-acid signaling but also through jasmonic-acid pathway activation. These findings clarify calcium-mediated mechanisms of drought defense in tree crops. Thus, calcium improves the drought response in the tea tree.

Overexpression of MdZAT5, an C2H2-Type Zinc Finger Protein, Regulates Anthocyanin Accumulation and Salt Stress Response in Apple Calli and Arabidopsis

Zinc finger proteins are widely involved and play an important role in plant growth and abiotic stress. In this research, MdZAT5, a gene encoding C2H2-type zinc finger protein, was cloned and investigated. The MdZAT5 was highly expressed in flower tissues by qRT-PCR analyses and GUS staining. Promoter analysis showed that MdZAT5 contained multiple response elements, and the expression levels of MdZAT5 were induced by various abiotic stress treatments. Overexpression of MdZAT5 in apple calli positively regulated anthocyanin accumulation by activating the expressions of anthocyanin biosynthesis-related genes. Overexpression of MdZAT5 in Arabidopsis also enhanced the accumulation of anthocyanin. In addition, MdZAT5 increased the sensitivity to salt stress in apple calli. Ectopic expression of MdZAT5 in Arabidopsis reduced the expression of salt-stress-related genes (AtNHX1 and AtABI1) and improved the sensitivity to salt stress. In conclusion, these results suggest that MdZAT5 plays a positive regulatory role in anthocyanin accumulation and negatively regulates salt resistance.

Pseudomonas syringae activates ZAT18 to inhibit salicylic acid accumulation by repressing EDS1 transcription for bacterial infection

Phytopathogens can manipulate plant hormone signaling to counteract immune responses; however, the underlying mechanism is mostly unclear. Here, we report that Pseudomonas syringae pv tomato (Pst) DC3000 induces expression of C2H2 zinc finger transcription factor ZAT18 in a jasmonic acid (JA)-signaling-dependent manner. Biochemical assays further confirmed that ZAT18 is a direct target of MYC2, which is a very important regulator in JA signaling. CRISPR/Cas9-generated zat18-cr mutants exhibited enhanced resistance to Pst DC3000, while overexpression of ZAT18 resulted in impaired disease resistance. Genetic characterization of ZAT18 mutants demonstrated that ZAT18 represses defense responses by inhibiting the accumulation of the key plant immune signaling molecule salicylic acid (SA), which is dependent on its EAR motif. ZAT18 exerted this inhibitory effect by directly repressing the transcription of Enhanced Disease Susceptibility 1 (EDS1), which is the key signaling component of pathogen-induced SA accumulation. Overexpression of ZAT18 resulted in decreased SA content, while loss of function of ZAT18 showed enhanced SA accumulation upon pathogen infection. Furthermore, enhanced resistance and SA content in zat18-cr mutants was abolished by the mutation in EDS1. Our data indicate that pathogens induce ZAT18 expression to repress the transcription of EDS1, further antagonising SA accumulation for bacterial infection.

Genetic Mapping and QTL Analysis of Stigma Color in Melon (Cucumis melo L.)

Melon is an important Cucurbitaceae crop. Field observations had shown that the green stigmas of melon are more attractive to pollinators than yellow stigmas. In this study, F₂ and F_2:3 populations obtained by crossing MR-1 (green stigma) and M4-7 (yellow stigma) were used for genetic analysis and mapping. A genetic map of 1,802.49 cm was constructed with 116 cleaved amplified polymorphism sequence (CAPS) markers. Two stable quantitative trait loci (QTLs) linked to the trait of stigma color were identified on chromosomes 2 (SC2.1) and 8 (SC8.1), respectively. An expanded F₂ population was used to narrow down the confidence regions of SC2.1 and SC8.1. As a result, SC2.1 was further mapped to a 3.6 cm region between CAPS markers S2M3 and S2B1-3, explaining 9.40% phenotypic variation. SC8.1 was mapped to a 3.7-cm region between CAPS markers S8E7 and S8H-1, explaining 25.92% phenotypic variation. This study broadens our understanding of the mechanisms of stigma color regulation and will be of benefit to the breeding of melon.

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

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

Comparative Expression Analysis of Stress-Inducible Candidate Genes in Response to Cold and Drought in Tea Plant [Camellia sinensis (L.) Kuntze]

Cold and drought are two of the most severe threats affecting the growth and productivity of the tea plant, limiting its global spread. Both stresses cause osmotic changes in the cells of the tea plant by decreasing their water potential. To develop cultivars that are tolerant to both stresses, it is essential to understand the genetic responses of tea plant to these two stresses, particularly in terms of the genes involved. In this study, we combined literature data with interspecific transcriptomic analyses (using Arabidopsis thaliana and Solanum lycopersicum) to choose genes related to cold tolerance. We identified 45 stress-inducible candidate genes associated with cold and drought responses in tea plants based on a comprehensive homologous detection method. Of these, nine were newly characterized by us, and 36 had previously been reported. The gene network analysis revealed upregulated expression in ICE1-related cluster of bHLH factors, HSP70/BAM5 connected genes (hexokinases, galactinol synthases, SnRK complex, etc.) indicating their possible co-expression. Using qRT-PCR we revealed that 10 genes were significantly upregulated in response to both cold and drought in tea plant: HSP70, GST, SUS1, DHN1, BMY5, bHLH102, GR-RBP3, ICE1, GOLS1, and GOLS3. SnRK1.2, HXK1/2, bHLH7/43/79/93 were specifically upregulated in cold, while RHL41, CAU1, Hydrolase22 were specifically upregulated in drought. Interestingly, the expression of CIP was higher in the recovery stage of both stresses, indicating its potentially important role in plant recovery after stress. In addition, some genes, such as DHN3, bHLH79, PEI54, SnRK1.2, SnRK1.3, and Hydrolase22, were significantly positively correlated between the cold and drought responses. CBF1, GOLS1, HXK2, and HXK3, by contrast, showed significantly negative correlations between the cold and drought responses. Our results provide valuable information and robust candidate genes for future functional analyses intended to improve the stress tolerance of the tea plant and other species.

Vascular Bundles Mediate Systemic Reactive Oxygen Signaling during Light Stress

Systemic signaling and systemic acquired acclimation (SAA) are essential for plant survival during episodes of environmental stress. Recent studies highlighted a key role for reactive oxygen species (ROS) signaling in mediating systemic responses and SAA during light stress in Arabidopsis (Arabidopsis thaliana). These studies further identified the RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD) protein as a key player in mediating rapid systemic ROS responses. Here, we report that tissue-specific expression of RBOHD in phloem or xylem parenchyma cells of the rbohD mutant restores systemic ROS signaling, systemic stress-response transcript expression, and SAA to a local treatment of light stress. We further demonstrate that RBOHD and RBOHF are both required for local and systemic ROS signaling at the vascular bundles of Arabidopsis. Taken together, our findings highlight a key role for RBOHD-driven ROS production at the vascular bundles of Arabidopsis in mediating light stress-induced systemic signaling and SAA. In addition, they suggest that the integration of ROS, calcium, electric, and hydraulic signals, during systemic signaling, occurs at the vascular bundles.

The Arabidopsis Transcriptome Responds Specifically and Dynamically to High Light Stress

The dynamic and specific transcriptome for high light (HL) stress in plants is poorly understood because heat has confounded previous studies. Here, we perform an in-depth temporal responsive transcriptome analysis and identify the core HL-responsive genes. By eliminating the effect of heat, we uncover a set of genes specifically regulated by high-intensity light-driven signaling. We find that 79% of HL-responsive genes restore their expression to baseline within a 14-h recovery period. Our study reveals that plants respond to HL through dynamic regulation of hormones, particularly abscisic acid (ABA), photosynthesis, and phenylpropanoid pathway genes. Blue/UV-A photoreceptors and phytochrome-interacting factor (PIF) genes are also responsive to HL. We further show that ABA biosynthesis-defective mutant nced3nced5, as well as pif4, pif5, pif4,5, and pif1,3,4,5 mutants, are hypersensitive to HL. Our study presents the dynamic and specific high-intensity light-driven transcriptional landscape in plants during HL stress.

Huang et al. present the specific and dynamic transcriptome for high-intensity light (HL) stress in plants. They identify the core HL-responsive genes and uncover that plants respond to HL by dynamically regulating hormones, anthocyanin, photosynthesis, photoreceptors, and PIF genes. They show that ABA and PIFs are required for HL response.

C2H2 Zinc Finger Proteins: Master Regulators of Abiotic Stress Responses in Plants

Abiotic stresses such as drought and salinity are major environmental factors that limit crop yields. Unraveling the molecular mechanisms underlying abiotic stress resistance is crucial for improving crop performance and increasing productivity under adverse environmental conditions. Zinc finger proteins, comprising one of the largest transcription factor families, are known for their finger-like structure and their ability to bind Zn2+. Zinc finger proteins are categorized into nine subfamilies based on their conserved Cys and His motifs, including the Cys2/His2-type (C2H2), C3H, C3HC4, C2HC5, C4HC3, C2HC, C4, C6, and C8 subfamilies. Over the past two decades, much progress has been made in understanding the roles of C2H2 zinc finger proteins in plant growth, development, and stress signal transduction. In this review, we focus on recent progress in elucidating the structures, functions, and classifications of plant C2H2 zinc finger proteins and their roles in abiotic stress responses.

Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.)

The C2H2 zinc finger protein (C2H2-ZFP) transcription factor family regulates the expression of a wide variety of genes in response to various developmental processes or abiotic stresses; however, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum). In this study, a total of 104 C2H2-ZFs were identified in an uneven distribution across the entire tomato genome, and include seven segmental duplication events. Based on their phylogenetic relationships, these genes were clustered into nine distinct categories analogous to those in Arabidopsis thaliana. High similarities were found between the exon–intron structures and conserved motifs of the genes within each group. Correspondingly, the expression patterns of the C2H2-ZF genes indicated that they function in different tissues and at different developmental stages. Additionally, quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 34 selected C2H2-ZFs are changed dramatically among the roots, stems, and leaves at different time points of a heat stress treatment, suggesting that the C2H2-ZFPs are extensively involved in the heat stress response but have potentially varying roles. These results form the basis for the further molecular and functional analysis of the C2H2-ZFPs, especially for those members that significantly varied under heat treatment, which may be targeted to improve the heat tolerance of tomato and other Solanaceae species.

Transcription Factor Networks in Leaves of Cichorium endivia: New Insights into the Relationship Between Photosynthesis and Leaf Development

Cichorium endivia is a leafy crop closely related to Lactuca sativa that comprises two major botanical varieties characterized by a high degree of intraspecific morphological variation: var. latifolium with broad leaves (escarole) and var. crispum with narrow crisp curly leaves (endive). To investigate the relationship between leaf morphology and photosynthetic activity, escaroles and endives were used as a crop model due to the striking morphological diversity of their leaves. We constructed a leaf database for transcription factors (TFs) and photosynthesis-related genes from a refined C. endivia transcriptome and used RNA-seq transcriptomic data from leaves of four commercial endive and escarole cultivars to explore transcription factor regulatory networks. Cluster and gene co-expression network (GCN) analyses identified two main anticorrelated modules that control photosynthesis. Analysis of the GCN network topological properties identified known and novel hub genes controlling photosynthesis, and candidate developmental genes at the boundaries between shape and function. Differential expression analysis between broad and curly leaves suggested three novel TFs putatively involved in leaf shape diversity. Physiological analysis of the photosynthesis properties and gene expression studies on broad and curly leaves provided new insights into the relationship between leaf shape and function.

Molecular Evolution and Interaction of Membrane Transport and Photoreception in Plants

Light is a vital regulator that controls physiological and cellular responses to regulate plant growth, development, yield, and quality. Light is the driving force for electron and ion transport in the thylakoid membrane and other membranes of plant cells. In different plant species and cell types, light activates photoreceptors, thereby modulating plasma membrane transport. Plants maximize their growth and photosynthesis by facilitating the coordinated regulation of ion channels, pumps, and co-transporters across membranes to fine-tune nutrient uptake. The signal-transducing functions associated with membrane transporters, pumps, and channels impart a complex array of mechanisms to regulate plant responses to light. The identification of light responsive membrane transport components and understanding of their potential interaction with photoreceptors will elucidate how light-activated signaling pathways optimize plant growth, production, and nutrition to the prevailing environmental changes. This review summarizes the mechanisms underlying the physiological and molecular regulations of light-induced membrane transport and their potential interaction with photoreceptors in a plant evolutionary and nutrition context. It will shed new light on plant ecological conservation as well as agricultural production and crop quality, bringing potential nutrition and health benefits to humans and animals.

The Roles of Arabidopsis C1-2i Subclass of C2H2-type Zinc-Finger Transcription Factors

The Cys2His2 (C2H2)-type zinc-finger protein (ZFP) family, which includes 176 members in Arabidopsis thaliana, is one of the largest families of putative transcription factors in plants. Of the Arabidopsis ZFP members, only 33 members are conserved in other eukaryotes, with 143 considered to be plant specific. C2H2-type ZFPs have been extensively studied and have been shown to play important roles in plant development and environmental stress responses by transcriptional regulation. The ethylene-responsive element binding-factor-associated amphiphilic repression (EAR) domain (GCC box) has been found to have a critical role in the tolerance response to abiotic stress. Many of the plant ZFPs containing the EAR domain, such as AZF1/2/3, ZAT7, ZAT10, and ZAT12, have been shown to function as transcriptional repressors. In this review, we mainly focus on the C1-2i subclass of C2H2 ZFPs and summarize the latest research into their roles in various stress responses. The role of C2H2-type ZFPs in response to the abiotic and biotic stress signaling network is not well explained, and amongst them, C1-2i is one of the better-characterized classifications in response to environmental stresses. These studies of the C1-2i subclass ought to furnish the basis for future studies to discover the pathways and receptors concerned in stress defense. Research has implied possible protein-protein interactions between members of C1-2i under various stresses, for which we have proposed a hypothetical model.

The role of C2H2 zinc finger proteins in plant responses to abiotic stresses

Abiotic stresses are important factors affecting plant growth and development and limiting agricultural production worldwide. Plants have evolved complex regulatory mechanisms to respond and adapt to constantly changing environmental conditions. C2H2 zinc finger proteins form a relatively large family of transcriptional regulators in plants. Recent studies have revealed that C2H2 zinc finger proteins function as key transcriptional regulators in plant responses to a wide spectrum of stress conditions, including extreme temperatures, salinity, drought, oxidative stress, excessive light and silique shattering. Here, we summarize recent functional analysis on C2H2 zinc finger proteins in plant responses to abiotic stresses and discuss their roles as part of a large regulatory network in the perception and responses by plants to different environmental stimuli.

Cscs encoding chorismate synthase is a candidate gene for leaf variegation mutation in cucumber

Variegation is a frequently observed genetic phenomenon in landscaping. In this study, an ethyl methanesulfonate induced variegated leaf (Csvl) mutant in cucumber (Cucumis sativus L.) was identified. The Csvl mutant displayed green-yellow-white variegation phenotype throughout the whole growth cycle, while the leaf of wild type plants was normal green. The photosynthetic pigment contents and photosynthetic parameters of Csvl was significantly lower than wild type. The cytology observation results showed that the mesophyll cells of Csvl mutant contained defective chloroplasts. Genetic analysis indicated that variegated leaf phenotype was monogenic recessive inheritance. MutMap and genotyping results revealed that Csa6G405290 (Cscs), encoding chorismate synthase, was the candidate gene for variegated leaf mutant in cucumber. The expression level of Cscs was similar between wild type and variegated leaf mutant leaves. Transcriptome profile analysis of leaves of Csvl mutant identified 183 candidate genes involved in variegated leaf development in cucumber, including genes that encode heat shock protein, zinc finger protein. Cscs may regulate variegated leaf in cucumber by interacting with these genes. In a word, these results revealed that Cscs might regulate the variegated leaf phenotype in cucumber.

Features of Ppd-B1 expression regulation and their impact on the flowering time of wheat near-isogenic lines

BACKGROUND

Photoperiod insensitive Ppd-1a alleles determine early flowering of wheat. Increased expression of homoeologous Ppd-D1a and Ppd-A1a result from deletions in the promoter region, and elevated expression of Ppd-B1a is determined by an increased copy number.

RESULTS

In this study, using bread wheat cultivars Sonora and PSL2, which contrast in flowering time, and near-isogenic lines resulting from their cross, "Ppd-m" and "Ppd-w" with Ppd-B1a introgressed from Sonora, we investigated the putative factors that influence Ppd-B1a expression. By analyzing the Ppd-B1a three distinct copies, we identified an indel and the two SNPs, which distinguished the investigated allele from other alleles with a copy number variation. We studied the expression of the Ppd-A1, Ppd-B1a, and Ppd-D1 genes along with genes that are involved in light perception (PhyA, PhyB, PhyC) and the flowering initiation (Vrn-1, TaFT1) and discussed their interactions. Expression of Ppd-B1a in the "Ppd-m" line, which flowered four days earlier than "Ppd-w", was significantly higher. We found PhyC to be up-regulated in lines with Ppd-B1a alleles. Expression of PhyC was higher in "Ppd-m". Microsatellite genotyping demonstrated that in the line "Ppd-m", there is an introgression in the pericentromeric region of chromosome 5B from the early flowering parental Sonora, while the "Ppd-w" does not have this introgression. FHY3/FAR1 is known to be located in this region. Expression of the transcription factor FHY3/FAR1 was higher in the "Ppd-m" line than in "Ppd-w", suggesting that FHY3/FAR1 is important for the wheat flowering time and may cause earlier flowering of "Ppd-m" as compared to "Ppd-w".

CONCLUSIONS

We propose that there is a positive bidirectional regulation of Ppd-B1a and PhyC with an FHY3/FAR1 contribution. The bidirectional regulation can be proposed for Ppd-A1a and Ppd-D1a. Using in silico analysis, we demonstrated that the specificity of the Ppd-B1 regulation compared to that of homoeologous genes involves not only a copy number variation but also distinct regulatory elements.

Melatonin alleviates chilling stress in cucumber seedlings by up-regulation of CsZat12 and modulation of polyamine and abscisic acid metabolism

To obtain new insights into the mechanisms of the positive effects of exogenous melatonin applications to cucumber seedlings during chilling, we investigated its role in regulating photosynthesis, the transcription level of csZat12 and the metabolism of polyamines (PAs) and of abscisic acid (ABA). The negative effects of chilling were clearly alleviated in cucumber seedlings by irrigation with 200 μM melatonin solution. This was evidenced by alleviation of the decline in net photosynthesis rate and also in electrolyte leakage in chilled plants. The reasons for this can be explained as follows. First, melatonin up-regulates CsZat12, an important stress-related gene. Second, melatonin increases the content of putrescine (Put) and spermidine (Spd) and stabilized spermine (Spm) by altering the activity of the PA metabolic enzymes. And, third, ABA is also involved in these effects as melatonin modulated the expression of the key ABA biosynthesis genes (CsNCED1 and CsNCED2) and also the key ABA catabolism genes (CsCYP707A1 and CsCYP707A2). This study provides new evidence suggesting melatonin mitigates chilling stress in cucumber by up-regulating the expression of CsZat12 and by modulating the metabolism of PAs and ABA.

Unraveling the early molecular and physiological mechanisms involved in response to phenanthrene exposure

BACKGROUND

Higher plants have to cope with increasing concentrations of pollutants of both natural and anthropogenic origin. Given their capacity to concentrate and metabolize various compounds including pollutants, plants can be used to treat environmental problems - a process called phytoremediation. However, the molecular mechanisms underlying the stabilization, the extraction, the accumulation and partial or complete degradation of pollutants by plants remain poorly understood.

RESULTS

Here, we determined the molecular events involved in the early plant response to phenanthrene, used as a model of polycyclic aromatic hydrocarbons. A transcriptomic and a metabolic analysis strongly suggest that energy availability is the crucial limiting factor leading to high and rapid transcriptional reprogramming that can ultimately lead to death. We show that the accumulation of phenanthrene in leaves inhibits electron transfer and photosynthesis within a few minutes, probably disrupting energy transformation.

CONCLUSION

This kinetic analysis improved the resolution of the transcriptome in the initial plant response to phenanthrene, identifying genes that are involved in primary processes set up to sense and detoxify this pollutant but also in molecular mechanisms used by the plant to cope with such harmful stress. The identification of first events involved in plant response to phenanthrene is a key step in the selection of candidates for further functional characterization, with the prospect of engineering efficient ecological detoxification systems for polycyclic aromatic hydrocarbons.

Genome-Wide Identification and Characterization of MicroRNAs and Target Genes in Lonicera japonica

MiRNAs function in post-transcriptional regulation of gene expression and play very important roles in plant development. Lonicera japonica is one of the important medicinal plants in China. However, few studies on the discovery of conserved and novel miRNAs from L. japonica were reported. In this study, we employed deep sequencing technology to identify miRNAs in leaf and flower tissues of L. japonica. A total of 22.97 million clean reads from flower and leaf tissues were obtained, which generated 146 conserved miRNAs distributed in 20 families and 110 novel miRNAs. Accordingly, 72 differentially expressed miRNAs (P≤0.001) between leaves and flowers and their potential target genes were identified and validated. The qRT-PCR validation showed that majority of the differentially expressed miRNAs showed significant tissue-specific expression in L. japonica. Furthermore, the miRNA-mRNA and mRNA-mRNA regulatory networks were constructed using Cytoscape software. Taken together, this study identified a large number of miRNAs and target genes in L. japonica, which not only provides the first global miRNA expression profiles, but also sheds light on functional genomics research on L. japonica in the future.

Identification of novel transcriptional regulators of Zat12 using comprehensive yeast one-hybrid screens

To appropriately acclimate to environmental stresses, plants have to rapidly activate a specific transcriptional program. Yet, the identity and function of many of the transcriptional regulators that mediate early responses to abiotic stress stimuli is still unknown. In this work we employed the promoter of the multi-stress-responsive zinc-finger protein Zat12 in yeast one-hybrid (Y1H) screens to identify early abiotic stress-responsive transcriptional regulators. Analysis of Zat12 promoter fragments fused to luciferase underlined an approximately 200 bp fragment responsive to NaCl and to reactive oxygen species (ROS). Using these segments and others as baits against Y1H control or stress Arabidopsis prey libraries, we identified 15 potential Zat12 transcriptional regulators. Among the prominent proteins identified were known transcription factors including bZIP29 and ANAC91 as well as unknown function proteins such as a homolog of the human USB1, a U6 small nuclear RNA (snRNA) processing protein, and dormancy/auxin-associated family protein 2 (DRM2). Altered expression of Zat12 during high light stress in the knockout mutants further indicated the involvement of these proteins in the regulation of Zat12. Using a state of the art microfluidic approach we showed that AtUSB1 and DRM2 can specifically bind dsDNA and were able to identify the preferred DNA-binding motif of all four proteins. Overall, the proteins identified in this work provide an important start point for charting the earliest signaling network of Zat12 and of other genes required for acclimation to abiotic stresses.

Laminarin modulates the chloroplast antioxidant system to enhance abiotic stress tolerance partially through the regulation of the defensin-like gene expression

Algae wall polysaccharide, laminarin (Lam), has an established role on induction of plant disease resistance. In this study, application of Lam increased Arabidopsis fresh weight and enhanced tolerance to salt and heat stress by stabilizing chloroplast under adverse environment. Transcriptome analysis indicated that, in addition to induced a large number of genes associated with the host defense, genes involved in the regulation of abiotic stress tolerance mostly the heat stress response constituted the largest group of the up-regulated genes. Lam induced expression of IRT1, ZIP8, and copper transporters involved in transport of Fe, Zn, Cu ions associated with the activity of chloroplast antioxidant system. Lam also up-regulated genes involved in the synthesis of terpenoid, a plastidial-derived secondary metabolite with antioxidant activity. Overexpression of a Lam-induced defensin like 202 (DEFL202) resulted in increased chloroplast stability under salt stress and increased plant growth activity after heat stress. Expression of antioxidant enzymes including SOD and ascorbate peroxidase (APX), photosystem PsbA-D1 and ABA-dependent responsive to desiccation 22 (RD22) was induced to higher levels in the transgenic seedlings. In sum, our results suggest that Lam is an potent inducer for induction of chloroplastic antioxidant activity. Lam affect plant abiotic stress tolerance partially through regulation of the DEFL-mediated pathway.

Ultra-fast alterations in mRNA levels uncover multiple players in light stress acclimation in plants

The acclimation of plants to changes in light intensity requires rapid responses at several different levels. These include biochemical and biophysical responses as well as alterations in the steady-state level of different transcripts and proteins. Recent studies utilizing promoter::reporter constructs suggested that transcriptional responses to changes in light intensity could occur within seconds, rates for which changes in mRNA expression are not routinely measured or functionally studied. To identify and characterize rapid changes in the steady-state level of different transcripts in response to light stress we performed RNA sequencing analysis of Arabidopsis thaliana plants subjected to light stress. Here we report that mRNA accumulation of 731 transcripts occurs as early as 20-60 sec following light stress application, and that at least five of these early response transcripts play an important biological role in the acclimation of plants to light stress. More than 20% of transcripts accumulating in plants within 20-60 sec of initiation of light stress are H2 O2 - and ABA-response transcripts, and the accumulation of several of these transcripts is inhibited by transcriptional inhibitors. In accordance with the association of rapid response transcripts with H2 O2 and ABA signaling, a mutant impaired in ABA sensing (abi-1) was found to be more tolerant to light stress, and the response of several of the rapid response transcripts was altered in mutants impaired in reactive oxygen metabolism. Our findings reveal that transcriptome reprogramming in plants could occur within seconds of initiation of abiotic stress and that this response could invoke known as well as unknown proteins and pathways.

Distinct palisade tissue development processes promoted by leaf autonomous signalling and long-distance signalling in Arabidopsis thaliana

Plants develop palisade tissue consisting of cylindrical mesophyll cells located at the adaxial side of leaves in response to high light. To understand high light signalling in palisade tissue development, we investigated leaf autonomous and long-distance signal responses of palisade tissue development using Arabidopsis thaliana. Illumination of a developing leaf with high light induced cell height elongation, whereas illumination of mature leaves with high light increased cell density and suppressed cell width expansion in palisade tissue of new leaves. Examination using phototropin1 phototropin2 showed that blue light signalling mediated by phototropins was involved in cell height elongation of the leaf autonomous response rather than the cell density increase induced by long-distance signalling. Hydrogen peroxide treatment induced cylindrical palisade tissue cell formation in both a leaf autonomous and long-distance manner, suggesting involvement of oxidative signals. Although constitutive expression of transcription factors involved in systemic-acquired acclimation to excess light, ZAT10 and ZAT12, induced cylindrical palisade tissue cell formation, knockout of these genes did not affect cylindrical palisade tissue cell formation. We conclude that two distinct signalling pathways - leaf autonomous signalling mostly dependent on blue light signalling and long-distance signalling from mature leaves that sense high light and oxidative stress - control palisade tissue development in A. thaliana.

Arabidopsis drought-induced protein Di19-3 participates in plant response to drought and high salinity stresses

Di19 (drought-induced protein19) family is a novel type of Cys2/His2 zinc-finger proteins. In this study, Arabidopsis Di19-3 was functionally characterized. The experimental results revealed that AtDi19-3 is a transcriptional activator, and could bind to the TACA(A/G)T sequence. AtDi19-3 expression in plants was remarkably induced by NaCl, mannitol and abscisic acid (ABA). T-DNA insertion mutation of AtDi19-3 results in an increase in plant tolerance to drought and high salinity stresses and ABA, whereas overexpression of AtDi19-3 leads to a drought-, salt- and ABA-sensitive phenotype of the transgenic plants. In the presence of NaCl, mannitol or ABA, rates of seed germination and cotyledon greening in Atdi19-3 mutant were higher, but in AtDi19-3 overexpression transgenic plants were lower than those in wild type. Roots of Atdi19-3 mutant seedlings were longer, but those of AtDi19-3 overexpression transgenic seedlings were shorter than those of wild type. Chlorophyll and proline contents in Atdi19-3 mutant were higher, but in AtDi19-3 overexpression seedlings were lower than those in wild type. Atdi19-3 mutant showed greater drought-tolerance, whereas AtDi19-3 overexpression transgenic plants exhibited more drought-sensitivity than wild type. Furthermore, expression of the genes related to ABA signaling pathway was altered in Atdi19-3 mutant and AtDi19-3 transgenic plants. These data suggest that AtDi19-3 may participate in plant response to drought and salt stresses in an ABA-dependent manner.

A novel rice C2H2-type zinc finger protein, ZFP36, is a key player involved in abscisic acid-induced antioxidant defence and oxidative stress tolerance in rice

C2H2-type zinc finger proteins (ZFPs) have been shown to play important roles in the responses of plants to oxidative and abiotic stresses, and different members of this family might have different roles during stresses. Here a novel abscisic acid (ABA)- and hydrogen peroxide (H₂O₂)-responsive C2H2-type ZFP gene, ZFP36, is identified in rice. The analyses of ZFP36-overexpressing and silenced transgenic rice plants showed that ZFP36 is involved in ABA-induced up-regulation of the expression and the activities of superoxide dismutase (SOD) and ascorbate peroxidase (APX). Overexpression of ZFP36 in rice plants was found to elevate the activities of antioxidant enzymes and to enhance the tolerance of rice plants to water stress and oxidative stress. In contrast, an RNA interference (RNAi) mutant of ZFP36 had lower activities of antioxidant enzymes and was more sensitive to water stress and oxidative stress. ABA-induced H₂O₂ production and ABA-activated mitogen-activated protein kinases (MAPKs) were shown to regulate the expression of ZFP36 in ABA signalling. On the other hand, ZFP36 also regulated the expression of NADPH oxidase genes, the production of H₂O₂, and the expression of OsMPK genes in ABA signalling. These results indicate that ZFP36 is required for ABA-induced antioxidant defence, for the tolerance of rice plants to water stress and oxidative stress, and for the regulation of the cross-talk between NADPH oxidase, H₂O₂, and MAPK in ABA signalling.

Transcriptome and metabolome analysis of plant sulfate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulfur, nitrogen and phosphorus nutritional responses in Arabidopsis

Sulfur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulfur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulfate starvation have been studied in the past, knowledge of the regulation of sulfur metabolism is still fragmentary. This work focuses on the discovery of candidates for regulatory genes such as transcription factors (TFs) using 'omics technologies. For this purpose a short term sulfate-starvation/re-supply approach was used. ATH1 microarray studies and metabolite determinations yielded 21 TFs which responded more than 2-fold at the transcriptional level to sulfate starvation. Categorization by response behaviors under sulfate-starvation/re-supply and other nutrient starvations such as nitrate and phosphate allowed determination of whether the TF genes are specific for or common between distinct mineral nutrient depletions. Extending this co-behavior analysis to the whole transcriptome data set enabled prediction of putative downstream genes. Additionally, combinations of transcriptome and metabolome data allowed identification of relationships between TFs and downstream responses, namely, expression changes in biosynthetic genes and subsequent metabolic responses. Effect chains on glucosinolate and polyamine biosynthesis are discussed in detail. The knowledge gained from this study provides a blueprint for an integrated analysis of transcriptomics and metabolomics and application for the identification of uncharacterized genes.

Transcriptome and metabolome analysis of plant sulfate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulfur, nitrogen and phosphorus nutritional responses in Arabidopsis

Sulfur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulfur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulfate starvation have been studied in the past, knowledge of the regulation of sulfur metabolism is still fragmentary. This work focuses on the discovery of candidates for regulatory genes such as transcription factors (TFs) using 'omics technologies. For this purpose a short term sulfate-starvation/re-supply approach was used. ATH1 microarray studies and metabolite determinations yielded 21 TFs which responded more than 2-fold at the transcriptional level to sulfate starvation. Categorization by response behaviors under sulfate-starvation/re-supply and other nutrient starvations such as nitrate and phosphate allowed determination of whether the TF genes are specific for or common between distinct mineral nutrient depletions. Extending this co-behavior analysis to the whole transcriptome data set enabled prediction of putative downstream genes. Additionally, combinations of transcriptome and metabolome data allowed identification of relationships between TFs and downstream responses, namely, expression changes in biosynthetic genes and subsequent metabolic responses. Effect chains on glucosinolate and polyamine biosynthesis are discussed in detail. The knowledge gained from this study provides a blueprint for an integrated analysis of transcriptomics and metabolomics and application for the identification of uncharacterized genes.

Expression of the high light-inducible Dunaliella LIP promoter in Chlamydomonas reinhardtii

The development of highly inducible promoters is critical for designing effective transformation systems for transgenic analyses. In this study, we investigated the promoter of the light-inducible protein gene (LIP) of the marine alga Dunaliella sp. LIPs are homologs of the early light-induced proteins (ELIPs) of Arabidopsis thaliana. DNA sequence analysis revealed that the LIP promoter contains several light-responsive motifs. Constructs containing progressive truncations of the LIP promoter fused with a Renilla luciferase gene were introduced into Chlamydomonas reinhardtii to identify the light-responsive region in the promoter. Transcription from the LIP promoter was stimulated by high light (HL) in a light intensity-dependent manner. In contrast, oxidative stress induced by chemicals had little effect on the LIP promoter, which implies that the LIP promoter is exclusively induced by high light. Truncation of the promoter to a -100 base pair (bp) region abrogated light inducibility, which suggests the presence of a negative cis-regulatory element upstream of the -100 bp fragment. The LIP promoter can be utilized in transgenic research to specifically select and propagate transgenic microalgae under high-light conditions.

A deficiency in chloroplastic ferredoxin 2 facilitates effective photosynthetic capacity during long-term high light acclimation in Arabidopsis thaliana

Photosynthetic electron transport is the major energy source for cellular metabolism in plants, and also has the potential to generate excess reactive oxygen species that cause irreversible damage to photosynthetic apparatus under adverse conditions. Ferredoxins (Fds), as the electron-distributing hub in the chloroplast, contribute to redox regulation and antioxidant defense. However, the steady-state levels of photosynthetic Fd decrease in plants when they are exposed to environmental stress conditions. To understand the effect of Fd down-regulation on plant growth, we characterized Arabidopsis thaliana plants lacking Fd2 (Fd2-KO) under long-term high light (HL) conditions. Unexpectedly, Fd2-KO plants exhibited efficient photosynthetic capacity and stable thylakoid protein complexes. At the transcriptional level, photoprotection-related genes were up-regulated more in the mutant plants, suggesting that knockout Fd2 lines possess a relatively effective photo-acclimatory responses involving enhanced plastid redox signaling. In contrast to the physiological characterization of Fd2-KO under short-term HL, the plastoquinone pool returned to a relatively balanced redox state via elevated PGR5-dependent cyclic electron flow during extended HL. fd2 pgr5 double mutant plants displayed severely impaired photosynthetic capacity under HL treatment, further supporting a role for PGR5 in adaptation to HL in the Fd2-KO plants. These results suggest potential benefits of reducing Fd levels in plants grown under long-term HL conditions.

Engineering drought tolerant tomato plants over-expressing BcZAT12 gene encoding a C₂H₂ zinc finger transcription factor

Efficient genetic transformation of cotyledonary explants of tomato (Solanum lycopersicum, cv. H-86, Kashi vishesh) was obtained. Disarmed Agrobacterium tumifaciens strain GV 3101 was used in conjugation with binary vector pBinAR containing a construct consisting of the coding sequence of the BcZAT12 gene under the regulatory control of the stress inducible Bclea1a promoter. ZAT12 encodes a C₂H₂ zinc finger protein which confers multiple abiotic stress tolerance to plants. Integration of ZAT12 gene into nuclear genome of individual kanamycin resistant transformed T₀ tomato lines was confirmed by Southern blot hybridization with segregation analysis of T(1) plants showing Mendelian inheritance of the transgene. Expression of ZAT12 in drought-stressed transformed tomato lines was verified in T₂ generation plants using RT-PCR. Of the six transformed tomato lines (ZT1-ZT6) the transformants ZT1 and ZT5 showed maximum expression of BcZAT12 gene transcripts when exposed to 7 days drought stress. Analysis of relative water content (RWC), electrolyte leakage (EL), chlorophyll colour index (CCI), H₂O₂ level and catalase activity suggested that tomato BcZAT12 transformants ZT1 and ZT5 have significantly increased levels of drought tolerance. These results suggest that BcZAT12 transformed tomato cv. H-86 has real potential for molecular breeding programs aimed at augmenting yield of tomato in regions affected with drought stress.

The heterologous expression in Arabidopsis of a chrysanthemum Cys2/His2 zinc finger protein gene confers salinity and drought tolerance

Zinc finger proteins (ZFPs) play an important role in plant growth and development. Here, we describe the isolation of CgZFP1, a Cys2/His2 (C(2)H(2)) ZFP gene, using RACE PCR from chrysanthemum, and the investigation of its function with ectopic expression in Arabidopsis. CgZFP1 contains two conserved C(2)H(2) regions, a nuclear localization domain (B box), a Leu-rich domain (L box) and a conserved DLN sequence (DLN box) close to its C-terminus. Its expression in the chrysanthemum leaf was strongly induced by salinity or drought, but not by ABA. Subcellular localization assay indicated that CgZFP1 protein is localized in nucleus in vivo. Yeast-one hybrid assay showed that CgZFP1 possesses transcriptional activation ability, heterologous expression of CgZFP1 conferred tolerance of transgenic Arabidopsis plants to both salinity and drought stresses. Under salinity stress, genes involved in osmotic adjustment, ROS scavenging, and ion homeostasis: Atlea3, AtP5CS2, AtProT1, and AtMnSOD, AtPOD, AtAPX1, and AtSOS1, AtSOS2, AtSOS3, AtNHX1 were enhanced in CgZFP1 transgenic Arabidopsis plants. Moreover, genes involved in the osmotic adjustment and oxidative stress responses: Atlea3, AtP5CS2, AtProT1, the aquaporin AtPIP2A, and AtMnSOD, AtPOD, AtAPX1 were induced in CgZFP1 transgenic Arabidopsis under drought stress. These results indicate CgZFP1 is an important regulator involved in the salt and drought stress response in plants.

Involvement of plant C(2)H(2)-type zinc finger transcription factors in stress responses

Abiotic and biotic stresses frequently impose constraints on plant distribution and affect agricultural productivity. Various aspects of the multiplicity and the complexity of stress responsive gene networks have been previously studied. Many of individual transcription factors in plants and their family classes that regulate the expression of several genes in responses to environmental stresses have been identified. One such class of transcription regulators is the C(2)H(2) class of zinc finger proteins. Numerous members of the C(2)H(2)-type zinc finger family have been shown to play diverse roles in the plant stress response and the hormone signal transduction. Transcription profiling analyses have demonstrated that the transcript level of many C(2)H(2)-type zinc finger proteins is elevated under different abiotic stress conditions such as low temperature, salt, drought, osmotic stress and oxidative stress. Some C(2)H(2)-type proteins are additionally involved in the biotic stress signaling pathway. Moreover, it has been reported that overexpression of some C(2)H(2)-type zinc finger protein genes resulted in both the activation of some stress-related genes and enhanced tolerance to various stresses. Current genetic studies have focused on possible interactions between different zinc finger transcription factors during stresses to regulate transcription. This review highlights the role of the C(2)H(2) class of the zinc finger proteins in regulating abiotic and biotic stress tolerance in the plants.

The chloroplast division mutant caa33 of Arabidopsis thaliana reveals the crucial impact of chloroplast homeostasis on stress acclimation and retrograde plastid-to-nucleus signaling

Retrograde plastid-to-nucleus signaling tightly controls and coordinates the nuclear and plastid gene expression that is required for plastid biogenesis and chloroplast activity. As chloroplasts act as sensors of environmental changes, plastid-derived signaling also modulates stress responses of plants by transferring stress-related signals and altering nuclear gene expression. Various mutant screens have been undertaken to identify constituents of plastid signaling pathways. Almost all mutations identified in these screens target plastid-specific but not extraplastidic functions. They have been suggested to define either genuine constituents of retrograde signaling pathways or components required for the synthesis of plastid signals. Here we report the characterization of the constitutive activator of AAA-ATPase (caa33) mutant, which reveals another way of how mutations that affect plastid functions may modulate retrograde plastid signaling. caa33 disturbs a plastid-specific function by impeding plastid division, and thereby perturbing plastid homeostasis. This results in preconditioning plants by activating the expression of stress genes, enhancing pathogen resistance and attenuating the capacity of the plant to respond to plastid signals. Our study reveals an intimate link between chloroplast activity and the susceptibility of the plant to stress, and emphasizes the need to consider the possible impact of preconditioning on retrograde plastid-to-nucleus signaling.

Comparison of transcriptional changes to chloroplast and mitochondrial perturbations reveals common and specific responses in Arabidopsis

Throughout the life of a plant, the biogenesis and fine-tuning of energy organelles is essential both under normal growth and stress conditions. Communication from organelle to nucleus is essential to adapt gene regulation and protein synthesis specifically to the current needs of the plant. This organelle-to-nuclear communication is termed retrograde signaling and has been studied extensively over the last decades. In this study we have used large-scale gene expression data sets relating to perturbations of chloroplast and mitochondrial function to gain further insights into plant retrograde signaling and how mitochondrial and chloroplast retrograde pathways interact and differ. Twenty seven studies were included that assess transcript profiles in response to chemical inhibition as well as genetic mutations of organellar proteins. The results show a highly significant overlap between gene expression changes triggered by chloroplast and mitochondrial perturbations. These overlapping gene expression changes appear to be common with general abiotic, biotic, and nutrient stresses. However, retrograde signaling pathways are capable of distinguishing the source of the perturbation as indicated by a statistical overrepresentation of changes in genes encoding proteins of the affected organelle. Organelle-specific overrepresented functional categories among others relate to energy metabolism and protein synthesis. Our analysis also suggests that WRKY transcription factors play a coordinating role on the interface of both organellar signaling pathways. Global comparison of the expression profiles for each experiment revealed that the recently identified chloroplast retrograde pathway using phospho-adenosine phosphate is possibly more related to mitochondrial than chloroplast perturbations. Furthermore, new marker genes have been identified that respond specifically to mitochondrial and/or chloroplast dysfunction.

Role of Linkers between Zinc Fingers in Spacing Recognition by Plant TFIIIA-Type Zinc-Finger Proteins

The EPF family of plant TFIIIA-type zinc-finger (ZF) proteins (ZPTs) is characterized by long linkers separating ZF motifs. We previously reported that two-fingered ZPTs bind to two tandem core sites that are separated by several base pairs, each ZF making contact with one core site. Here we report further characterization of DNA-binding activities of ZPTs using four family members, ZPT2-14, ZPT2-7, ZPT2-8, and ZPT2-2, having inter-ZF linkers of different lengths and sequences, to investigate the correlation of the length and/or sequence of the linker with preference for the spacing between core sites in target DNAs. Selected and amplified binding site (SAAB)-imprinting assays and gel mobility shift assays prompted three conclusions. (1) The four ZPTs have common specificity for core binding sites-two AGT(G)/(C)ACTs separated by several nucleotides. (2) The four ZPTs prefer a spacing of 10 bases between the core sites, but each ZPT has its own preference for suboptimal spacing. (3) At a particular spacing, two zinc fingers may bind to the core sites on both strands. The results provide new information about how the diversity in linker length/sequence affects DNA-sequence recognition in this protein family.

Integration of polyamines in the cold acclimation response

Temperature is one of the most important environmental factors limiting the geographical distribution of plants and accounts for significant reductions in the yield of agriculturally important crops. Low temperature damages many plant species, especially those adapted to tropical climates. In contrast, some species from temperate regions are able to develop freezing tolerance in response to low-non-freezing temperature, an adaptive process named cold acclimation. Numerous molecular, biochemical and physiological changes occur during cold acclimation, most of them being associated with significant changes in gene expression and metabolite profiles. During recent years, transcriptomic and metabolomic approaches have allowed the identification of cold-responsive genes and main metabolites which accumulate in plants exposed to cold. The obtained data support the previously held idea that polyamines (PAs) are involved in plant responses to cold, although their specific role is still not well understood. In this review, we synthesize published data regarding PA-responses to cold stress and integrate them with global transcriptional and metabolic changes. The potential of PA genetic engineering for the development of plants resistant to cold and freezing temperatures, and their plausible mechanisms of action are also discussed.

Interplay between low-temperature pathways and light reduction

Low temperature is one of the major factors that adversely affect crop yields by causing restraints on plant growth and productivity. However, most temperate plants have the ability to acclimate to cooler temperatures. Cold acclimation is a process which increases the freezing tolerance of an organism after exposure to low, non-freezing temperatures. The main trigger is a decrease in temperature levels, but light reduction has also been shown to have an important impact on acquired tolerance. Since the lowest temperatures are commonly reached during the night hours in winter time and is an annually recurring event, a favorable trait for plants is the possibility of sensing an imminent cold period. Consequently, extensive crosstalk between light- and temperature signaling pathways has been demonstrated and in this review interesting interaction points that have been previously reported in the literature are highlighted.

A mutation in the Arabidopsis mTERF-related plastid protein SOLDAT10 activates retrograde signaling and suppresses (1)O(2)-induced cell death

The conditional flu mutant of Arabidopsis thaliana generates singlet oxygen ((1)O(2)) in plastids during a dark-to-light shift. Seedlings of flu bleach and die, whereas mature plants stop growing and develop macroscopic necrotic lesions. Several suppressor mutants, dubbed singlet oxygen-linked death activator (soldat), were identified that abrogate (1)O(2)-mediated cell death of flu seedlings. One of the soldat mutations, soldat10, affects a gene encoding a plastid-localized protein related to the human mitochondrial transcription termination factor mTERF. As a consequence of this mutation, plastid-specific rRNA levels decrease and protein synthesis in plastids of soldat10 is attenuated. This disruption of chloroplast homeostasis in soldat10 seedlings affects communication between chloroplasts and the nucleus and leads to changes in the steady-state concentration of nuclear gene transcripts. The soldat10 seedlings suffer from mild photo-oxidative stress, as indicated by the constitutive up-regulation of stress-related genes. Even though soldat10/flu seedlings overaccumulate the photosensitizer protochlorophyllide in the dark and activate the expression of (1)O(2)-responsive genes after a dark-to-light shift they do not show a (1)O(2)-dependent cell death response. Disturbance of chloroplast homeostasis in emerging soldat10/flu seedlings seems to antagonize a subsequent (1)O(2)-mediated cell death response without suppressing (1)O(2)-dependent retrograde signaling. The results of this work reveal the unexpected complexity of what is commonly referred to as 'plastid signaling'.

Temporal expression patterns of hormone metabolism genes during imbibition of Arabidopsis thaliana seeds: a comparative study on dormant and non-dormant accessions

Seed imbibition is a prerequisite for subsequent dormancy and germination control. Here, we investigated imbibition responses of Arabidopsis seeds by transcriptomic and hormone profile analyses using dormant [Cape Verde Islands (Cvi)] and non-dormant [Columbia (Col)] accessions. Once imbibed, seeds of both accessions swelled most up to 3 h, reflecting water uptake. Microarray analysis showed that in both accessions, seeds imbibed for 15 min, 30 min and 1 h were less active in gene expression than at 3 h. More than 2,000 genes were either up-regulated or down-regulated in seeds imbibed for 3 h. Some genes up-regulated at 3 h were already induced in seeds imbibed for 1 h, suggestive of genome reprogramming early after the onset of imbibition. Imbibition-induced genes in seeds imbibed for 3 h included those up-regulated in both Col and Cvi (common) or unique to either accession (accession specific). Up-regulated genes that were both common and Cvi-specific were over-represented for sugar metabolism and the pentose phosphate pathway, whereas Col-specific genes were over-represented for ribosomal protein genes. Quantification of plant hormones showed that ABA and salicylic acid (SA) contents were higher, but gibberellin A(4) (GA(4)), N(6)-(Delta(2)-isopentenyl)adenine (iP), jasmonic acid (JA), JA-isoleucine (JA-Ile) and IAA were lower in imbibed seeds of Cvi compared with Col. In addition, changes in IAA and JA were initiated before 1 h, whereas ABA and JA-Ile declined 3 h after the onset of imbibition. An increase in GA(4) and iP appeared to be correlated temporally with the initiation of secondary water uptake, which marks the completion of germination.

Characterization of soldat8, a suppressor of singlet oxygen-induced cell death in Arabidopsis seedlings

The flu mutant of Arabidopsis thaliana overaccumulates in the dark the immediate precursor of chlorophyllide, protochlorophyllide (Pchlide), a potent photosensitizer, that upon illumination generates singlet oxygen ((1)O2). Once (1)O2 has been released in plastids of the flu mutant, mature plants stop growing, while seedlings die. Several suppressor mutations, dubbed singlet oxygen-linked death activator (soldat), were identified that specifically abrogate (1)O2-mediated stress responses in young flu seedlings without grossly affecting (1)O2-mediated stress responses of mature flu plants. One of the soldat mutations, soldat8, was shown to impair a gene encoding the SIGMA6 factor of the plastid RNA polymerase. Reintroduction of a wild-type copy of the SOLDAT8 gene into the soldat8/flu mutant restored the phenotype of the flu parental line. In contrast to flu, seedlings of soldat8/flu did not bleach when grown under non-permissive dark/light conditions, despite their continuous overaccumulation of the photosensitizer Pchlide in the dark. The activity of SIGMA6 is confined primarily to the very early stage of seedling development. Inactivation of SIGMA6 in soldat8 mutants disturbed plastid homeostasis, drastically reduced the non-photochemical quenching capacity and enhanced the light sensitivity of young soldat8 seedlings. Surprisingly, after being grown under very low light, soldat8 seedlings showed an enhanced resistance against a subsequent severe light stress that was significantly higher than in wild-type seedlings. In order to reach a similar enhanced stress resistance, wild-type seedlings had to be exposed to a brief higher light treatment that triggered an acclimatory response. Such a mild pre-stress treatment did not further enhance the stress resistance of soldat8 seedlings. Suppression of (1)O2-mediated cell death in young flu/soldat8 seedlings seems to be due to a transiently enhanced acclimation at the beginning of seedling development caused by the initial disturbance of plastid homeostasis.

Sensing and responding to excess light

Plants and algae often absorb too much light-more than they can actually use in photosynthesis. To prevent photo-oxidative damage and to acclimate to changes in their environment, photosynthetic organisms have evolved direct and indirect mechanisms for sensing and responding to excess light. Photoreceptors such as phototropin, neochrome, and cryptochrome can sense excess light directly and relay signals for chloroplast movement and gene expression responses. Indirect sensing of excess light through biochemical and metabolic signals can be transduced into local responses within chloroplasts, into changes in nuclear gene expression via retrograde signaling pathways, or even into systemic responses, all of which are associated with photoacclimation.

Systemic and intracellular responses to photooxidative stress in Arabidopsis

As the sun tracks daily through the sky from east to west, different parts of the canopy are exposed to high light (HL). The extent of and mechanisms by which a systemic acquired acclimation (SAA) response might preacclimate shaded leaves that will be subsequently exposed to full sunlight is largely undefined. We investigated the role of an Arabidopsis thaliana zinc finger transcription factor, ZAT10, in SAA. ZAT10 overexpression resulted in enhanced tolerance to photoinhibitory light and exogenous H2O2, increased expression of antioxidative genes whose products are targeted to multiple subcellular compartments. Partial HL exposure of a leaf or leaves rapidly induced ZAT10 mRNA in distal, shaded photosynthetic tissues, including the floral stem, cauline leaves, and rosette, but not in roots. Fully 86% of fivefold HL-upregulated and 71% of HL-downregulated genes were induced and repressed, respectively, in distal, shaded leaves. Between 15 and 23% of genes whose expression changed in the HL and/or distal tissues were coexpressed in the ZAT10 overexpression plants, implicating ZAT10 in modulating the expression of SAA-regulated genes. The SAA response was detectable in plants with mutations in abscisic acid, methyl jasmonate, or salicylic acid synthesis or perception, and systemic H2O2 diffusion was not detected. Hence, SAA is distinct from pathogen-stimulated systemic acquired resistance and apparently involves a novel signal or combination of signals that preacclimate photosynthetic tissues to HL.

Phosphate homeostasis and root development in Arabidopsis are synchronized by the zinc finger transcription factor ZAT6

Phosphorus availability is limited in many natural ecosystems. Plants adapt to phosphate (Pi) deficiency by complex molecular processes. There is growing evidence suggesting that transcription factors are key components in the regulation of these processes. In this study, we characterized the function of ZAT6 (zinc finger of Arabidopsis 6), a cysteine-2/histidine-2 zinc finger transcription factor that is responsive to Pi stress. ZAT6 is induced during Pi starvation and localizes to the nucleus. While the RNAi suppression of ZAT6 appeared to be lethal, its overexpression affects root development and retards seedling growth as a result of decreased Pi acquisition. The ZAT6 overexpression also resulted in altered root architecture of older plants, with consequent changes in Pi acquisition. These results indicate that ZAT6 regulates root development independent of the Pi status of the plant, thereby influencing Pi acquisition and homeostasis. In addition, the expression of several Pi starvation-responsive genes was decreased in ZAT6 overexpressing plants, thereby confirming the role of ZAT6 in regulating Pi homeostasis. This study thus indicates that ZAT6 is a repressor of primary root growth and regulates Pi homeostasis through the control of root architecture. To our knowledge, ZAT6 is the first cysteine-2/histidine-2 zinc finger transcription factor reported to regulate root development and nutrient stress responses.