Minimal influence of G-protein null mutations on ozone-induced changes in gene expression, foliar injury, gas exchange and peroxidase activity in Arabidopsis thaliana L

Pivotal role of heterotrimeric G protein in the crosstalk between sugar signaling and abiotic stress response in plants

Heterotrimeric G-proteins are key modulators of multiple signaling and developmental pathways in plants, in which they act as molecular switches to engage in transmitting various stimuli signals from outside into the cells. Substantial studies have identified G proteins as essential components of the organismal response to abiotic stress, leading to adaptation and survival in plants. Meanwhile, sugars are also well acknowledged key players in stress perception, signaling, and gene expression regulation. Connections between the two significant signaling pathways in stress response are of interest to a general audience in plant biology. In this article, advances unraveling a pivotal role of G proteins in the process of sugar signals outside the cells being translated into the operation of autophagy in cells during stress are reviewed. In addition, we have presented recent findings on G proteins regulating the response to drought, salt, alkali, cold, heat and other abiotic stresses. Perspectives on G-protein research are also provided in the end. Since G protein signaling regulates many agronomic traits, elucidation of detailed mechanism of the related pathways would provide useful insights for the breeding of abiotic stress resistant and high-yield crops.

Elevated tropospheric ozone and crop production: potential negative effects and plant defense mechanisms

Ozone (O3) levels on Earth are increasing because of anthropogenic activities and natural processes. Ozone enters plants through the leaves, leading to the overgeneration of reactive oxygen species (ROS) in the mesophyll and guard cell walls. ROS can damage chloroplast ultrastructure and block photosynthetic electron transport. Ozone can lead to stomatal closure and alter stomatal conductance, thereby hindering carbon dioxide (CO2) fixation. Ozone-induced leaf chlorosis is common. All of these factors lead to a reduction in photosynthesis under O3 stress. Long-term exposure to high concentrations of O3 disrupts plant physiological processes, including water and nutrient uptake, respiration, and translocation of assimilates and metabolites. As a result, plant growth and reproductive performance are negatively affected. Thus, reduction in crop yield and deterioration of crop quality are the greatest effects of O3 stress on plants. Increased rates of hydrogen peroxide accumulation, lipid peroxidation, and ion leakage are the common indicators of oxidative damage in plants exposed to O3 stress. Ozone disrupts the antioxidant defense system of plants by disturbing enzymatic activity and non-enzymatic antioxidant content. Improving photosynthetic pathways, various physiological processes, antioxidant defense, and phytohormone regulation, which can be achieved through various approaches, have been reported as vital strategies for improving O3 stress tolerance in plants. In plants, O3 stress can be mitigated in several ways. However, improvements in crop management practices, CO2 fertilization, using chemical elicitors, nutrient management, and the selection of tolerant crop varieties have been documented to mitigate O3 stress in different plant species. In this review, the responses of O3-exposed plants are summarized, and different mitigation strategies to decrease O3 stress-induced damage and crop losses are discussed. Further research should be conducted to determine methods to mitigate crop loss, enhance plant antioxidant defenses, modify physiological characteristics, and apply protectants.

Regulating Vapor Pressure Deficit and Soil Moisture Improves Tomato and Cucumber Plant Growth and Water Productivity in the Greenhouse

Atmospheric vapor pressure deficit (VPD) is the driving force that regulates the rate of water transport within plants. Under High VPD (HVPD), plants always reduce their photosynthesis rate and close their stomata. Experiments were performed under greenhouse conditions with cucumber and tomato plants to identify the regulatory effect of VPD on plant water capacity. Treatments included two levels of soil water (100% and 60% field capacity [FC]) combined with two levels of VPD (LVPD and HVPD). Results indicated that with 60%FC, the plant heights of tomato and cucumber were enhanced under LVPD compared with those under HVPD. With 60%FC, relative leaf water contents under LVPD increased by 11% compared with those under HVPD. Furthermore, LVPD significantly improved the photosynthetic capacity of the two crops and changed their stress responses. Our results indicated that LVPD at different soil moisture levels reduced irrigation demand under greenhouse conditions. This approach can be applied in water management in greenhouse vegetable production in China and other regions of the world with temperate continental climates.

Metabolic and physiological alterations indicate that the tropical broadleaf tree Eugenia uniflora L. is sensitive to ozone

Eugenia uniflora L. is an important fruit tree native to tropical South America that adapts to different habitats, thanks to its metabolic diversity and ability to adjust the leaf antioxidant metabolism. We hypothesized that this metabolic diversity would also enable E. uniflora to avoid oxidative damage and tolerate the enhanced ozone (O3) concentrations that have been registered in the (sub)tropics. We investigated whether carbohydrates, polyphenols and antioxidants are altered and markers of oxidative damage (ROS accumulation, alterations in leaf gas exchange, growth and biomass production) are detected in plants exposed to two levels of O₃ (ambient air and twice elevated ozone level in a O₃-FACE system for 75 days). Phytotoxic O₃ dose above a threshold of 0 nmol m^-2 s^-1 (POD0) and accumulated exposure above 40 ppb (AOT40) were 3.6 mmol m^-2 and 14.898 ppb h at ambient, and 4.7 mmol m^-2 and 43.881 ppb h at elevated O₃. Twenty-seven primary metabolites and 16 phenolic compounds were detected in the leaves. Contrary to the proposed hypothesis that tropical broadleaf trees are relatively O₃ tolerant, we concluded that E. uniflora plants are sensitive to elevated O₃ concentrations. Experimental POD0 values were lower than the critical levels for visible foliar O₃, because of low stomatal conductance. In spite of this low stomatal O₃ uptake, we found classic O₃ injury, e.g. reduction in carbohydrates and fatty acids concentrations; non-significant changes in the polyphenol profile; inefficient antioxidant responses; increased contents of ROS and indicators of lipid peroxidation; reductions in stomatal conductance, net photosynthesis, root/shoot ratio and height growth. However, we also found some compensation mechanisms, e.g. increased leaf concentration of polyols for protecting the membranes, and increased leaf number for compensating the decline of photosynthetic rate. These results help filling the knowledge gap about tropical tree responses to O₃.

Heterotrimeric G protein signalling in plant biotic and abiotic stress response

Heterotrimeric G proteins act as molecular switches to participate in transmitting various stimuli signals from outside of cells. G proteins have three subunits, Gα, Gβ and Gγ, which function mutually to modulate many biological processes in plants, including plant growth and development, as well as biotic and abiotic stress responses. In plants, the number of Gγ subunits is larger than that of the α and β subunits. Based on recent breakthroughs in studies of plant G protein signal perception, transduction and downstream effectors, this review summarizes and analyses the connections between different subunits and the interactions of G proteins with other signalling pathways, especially in plant biotic and abiotic stress responses. Based on current progress and unresolved questions in the field, we also suggest future research directions on G proteins in plants.

Heterotrimeric G-protein α subunit (RGA1) regulates tiller development, yield, cell wall, nitrogen response and biotic stress in rice

G-proteins are implicated in plant productivity, but their genome-wide roles in regulating agronomically important traits remain uncharacterized. Transcriptomic analyses of rice G-protein alpha subunit mutant (rga1) revealed 2270 differentially expressed genes (DEGs) including those involved in C/N and lipid metabolism, cell wall, hormones and stress. Many DEGs were associated with root, leaf, culm, inflorescence, panicle, grain yield and heading date. The mutant performed better in total weight of filled grains, ratio of filled to unfilled grains and tillers per plant. Protein–protein interaction (PPI) network analysis using experimentally validated interactors revealed many RGA1-responsive genes involved in tiller development. qPCR validated the differential expression of genes involved in strigolactone-mediated tiller formation and grain development. Further, the mutant growth and biomass were unaffected by submergence indicating its role in submergence response. Transcription factor network analysis revealed the importance of RGA1 in nitrogen signaling with DEGs such as Nin-like, WRKY, NAC, bHLH families, nitrite reductase, glutamine synthetase, OsCIPK23 and urea transporter. Sub-clustering of DEGs-associated PPI network revealed that RGA1 regulates metabolism, stress and gene regulation among others. Predicted rice G-protein networks mapped DEGs and revealed potential effectors. Thus, this study expands the roles of RGA1 to agronomically important traits and reveals their underlying processes.

Flexible functional interactions between G-protein subunits contribute to the specificity of plant responses

Plants being sessile integrate information from a variety of endogenous and external cues simultaneously to optimize growth and development. This necessitates the signaling networks in plants to be highly dynamic and flexible. One such network involves heterotrimeric G-proteins comprised of Gα, Gβ, and Gγ subunits, which influence many aspects of growth, development, and stress response pathways. In plants such as Arabidopsis, a relatively simple repertoire of G-proteins comprised of one canonical and three extra-large Gα, one Gβ and three Gγ subunits exists. Because the Gβ and Gγ proteins form obligate dimers, the phenotypes of plants lacking the sole Gβ or all Gγ genes are similar, as expected. However, Gα proteins can exist either as monomers or in a complex with Gβγ, and the details of combinatorial genetic and physiological interactions of different Gα proteins with the sole Gβ remain unexplored. To evaluate such flexible, signal-dependent interactions and their contribution toward eliciting a specific response, we have generated Arabidopsis mutants lacking specific combinations of Gα and Gβ genes, performed extensive phenotypic analysis, and evaluated the results in the context of subunit usage and interaction specificity. Our data show that multiple mechanistic modes, and in some cases complex epistatic relationships, exist depending on the signal-dependent interactions between the Gα and Gβ proteins. This suggests that, despite their limited numbers, the inherent flexibility of plant G-protein networks provides for the adaptability needed to survive under continuously changing environments.

Genetic and Systematic Approaches Toward G Protein-Coupled Abiotic Stress Signaling in Plants

Heterotrimeric G protein, composed of Gα, Gβ, and Gγ subunits, modulates plant adaptations to environmental stresses such as high salinity, drought, extreme temperatures and high light intensity. Most of these evidence were however derived solely from conventional genetics methods with which stress-associated phenotypes were compared between wild type and various G protein mutant plants. Recent advances in systematic approaches, mainly transcriptome and proteome, have contributed to in-depth understanding of molecular linkages between G proteins and environmental changes. Here, we update our knowledge on the roles of G proteins in abiotic stress responses. Furthermore, we highlight the current whole genome studies and integrated omics approach to better understand the fundamental G protein functions involved in abiotic stress responses. It is our purpose here to bridge the gap between molecular mechanisms in G protein science and stress biology and pave the way toward crop improvement researches in the future.

Understanding and improving global crop response to ozone pollution

Concentrations of ground-level ozone ([O3 ]) over much of the Earth's land surface have more than doubled since pre-industrial times. The air pollutant is highly variable over time and space, which makes it difficult to assess the average agronomic and economic impacts of the pollutant as well as to breed crops for O3 tolerance. Recent modeling efforts have improved quantitative understanding of the effects of current and future [O3 ] on global crop productivity, and experimental advances have improved understanding of the cellular O3 sensing, signaling and response mechanisms. This work provides the fundamental background and justification for breeding and biotechnological approaches for improving O3 tolerance in crops. There is considerable within-species variation in O3 tolerance in crops, which has been used to create mapping populations for screening. Quantitative trait loci (QTL) for O3 tolerance have been identified in model and crop species, and although none has been cloned to date, transcript profiling experiments have identified candidate genes associated with QTL. Biotechnological strategies for improving O3 tolerance are also being tested, although there is considerable research to be done before O3 -tolerant germplasm is available to growers for most crops. Strategies to improve O3 tolerance in crops have been hampered by the lack of translation of laboratory experiments to the field, and the lack of correlation between visual leaf-level O3 damage and yield loss to O3 stress. Future efforts to screen mapping populations in the field and to identify more promising phenotypes for O3 tolerance are needed.

On the effects of alternative optima in context-specific metabolic model predictions

The integration of experimental data into genome-scale metabolic models can greatly improve flux predictions. This is achieved by restricting predictions to a more realistic context-specific domain, like a particular cell or tissue type. Several computational approaches to integrate data have been proposed-generally obtaining context-specific (sub)models or flux distributions. However, these approaches may lead to a multitude of equally valid but potentially different models or flux distributions, due to possible alternative optima in the underlying optimization problems. Although this issue introduces ambiguity in context-specific predictions, it has not been generally recognized, especially in the case of model reconstructions. In this study, we analyze the impact of alternative optima in four state-of-the-art context-specific data integration approaches, providing both flux distributions and/or metabolic models. To this end, we present three computational methods and apply them to two particular case studies: leaf-specific predictions from the integration of gene expression data in a metabolic model of Arabidopsis thaliana, and liver-specific reconstructions derived from a human model with various experimental data sources. The application of these methods allows us to obtain the following results: (i) we sample the space of alternative flux distributions in the leaf- and the liver-specific case and quantify the ambiguity of the predictions. In addition, we show how the inclusion of ℓ1-regularization during data integration reduces the ambiguity in both cases. (ii) We generate sets of alternative leaf- and liver-specific models that are optimal to each one of the evaluated model reconstruction approaches. We demonstrate that alternative models of the same context contain a marked fraction of disparate reactions. Further, we show that a careful balance between model sparsity and metabolic functionality helps in reducing the discrepancies between alternative models. Finally, our findings indicate that alternative optima must be taken into account for rendering the context-specific metabolic model predictions less ambiguous.

Ligand-induced dynamics of heterotrimeric G protein-coupled receptor-like kinase complexes

Background

Arabidopsis, 7-transmembrane Regulator of G signaling protein 1 (AtRGS1) modulates canonical G protein signaling by promoting the inactive state of heterotrimeric G protein complex on the plasma membrane. It is known that plant leucine-rich repeat receptor–like kinases (LRR RLKs) phosphorylate AtRGS1 in vitro but little is known about the in vivo interaction, molecular dynamics, or the cellular consequences of this interaction.

Methods

Therefore, a subset of the known RLKs that phosphorylate AtRGS1 were selected for elucidation, namely, BAK1, BIR1, FLS2. Several microscopies for both static and dynamic protein-protein interactions were used to follow in vivo interactions between the RLKs and AtRGS1 after the presentation of the Pathogen-associated Molecular Pattern, Flagellin 22 (Flg22). These microscopies included Förster Resonance Energy Transfer, Bimolecular Fluoresence Complementation, and Cross Number and Brightness Fluorescence Correlation Spectroscopy. In addition, reactive oxygen species and calcium changes in living cells were quantitated using luminometry and R-GECO1 microscopy.

Results

The LRR RLKs BAK1 and BIR1, interact with AtRGS1 at the plasma membrane. The RLK ligand flg22 sets BAK1 in motion toward AtRGS1 and BIR1 away, both returning to the baseline orientations by 10 minutes. The C-terminal tail of AtRGS1 is important for the interaction with BAK1 and for the tempo of the AtRGS1/BIR1 dynamics. This window of time corresponds to the flg22-induced transient production of reactive oxygen species and calcium release which are both attenuated in the rgs1 and the bak1 null mutants.

Conclusions

A temporal model of these interactions is proposed. flg22 binding induces nearly instantaneous dimerization between FLS2 and BAK1. Phosphorylated BAK1 interacts with and enables AtRGS1 to move away from BIR1 and AtRGS1 becomes phosphorylated leading to its endocytosis thus leading to de-repression by permitting AtGPA1 to exchange GDP for GTP. Finally, the G protein complex becomes dissociated thus AGB1 interacts with its effector proteins leading to changes in reactive oxygen species and calcium.

Predicted Functional Implications of Phosphorylation of Regulator of G Protein Signaling Protein in Plants

Heterotrimeric G proteins function in development, biotic, and abiotic stress responses, hormone signaling as well as sugar sensing. We previously proposed that discrimination of these various external signals in the G protein pathway is accomplished in plants by membrane-localized receptor-like kinases (RLKs) rather than G-protein-coupled receptors. Arabidopsis thaliana Regulator of G Signaling protein 1 (AtRGS1) modulates G protein activation and is phosphorylated by several RLKs and by WITH-NO-LYSINE kinases (WNKs). Here, a combination of in vitro kinase assays, mass spectrometry, and computational bioinformatics identified and functionally prioritized phosphorylation sites in AtRGS1. Phosphosites for two more RLKs (BRL3 and PEPR1) were identified and added to the AtRGS1 phosphorylation profile. Bioinformatics analyses revealed that RLKs and WNK kinases phosphorylate plant RGS proteins within regions that are conserved across eukaryotes and at a high frequency. Four phospho-sites among 14 identified are proximal to equivalent mammalian phosphosites that impact RGS function, including: pS437 and pT267 in GmRGS2, and pS339 and pS436 in AtRGS1. Based on these analyses, we propose that pS437 and pS436 regulate GmRGS2 and AtRGS1 protein interactions and/or localization, whereas pT267 is important for modulation of GmRGS2 GAP activity and localization. Moreover, pS339 most likely affects AtRGS1 activation.

The ROS Wheel: Refining ROS Transcriptional Footprints

In the last decade, microarray studies have delivered extensive inventories of transcriptome-wide changes in messenger RNA levels provoked by various types of oxidative stress in Arabidopsis (Arabidopsis thaliana). Previous cross-study comparisons indicated how different types of reactive oxygen species (ROS) and their subcellular accumulation sites are able to reshape the transcriptome in specific manners. However, these analyses often employed simplistic statistical frameworks that are not compatible with large-scale analyses. Here, we reanalyzed a total of 79 Affymetrix ATH1 microarray studies of redox homeostasis perturbation experiments. To create hierarchy in such a high number of transcriptomic data sets, all transcriptional profiles were clustered on the overlap extent of their differentially expressed transcripts. Subsequently, meta-analysis determined a single magnitude of differential expression across studies and identified common transcriptional footprints per cluster. The resulting transcriptional footprints revealed the regulation of various metabolic pathways and gene families. The RESPIRATORY BURST OXIDASE HOMOLOG F-mediated respiratory burst had a major impact and was a converging point among several studies. Conversely, the timing of the oxidative stress response was a determining factor in shaping different transcriptome footprints. Our study emphasizes the need to interpret transcriptomic data sets in a systematic context, where initial, specific stress triggers can converge to common, aspecific transcriptional changes. We believe that these refined transcriptional footprints provide a valuable resource for assessing the involvement of ROS in biological processes in plants.

CCor: A whole genome network-based similarity measure between two genes

Measuring the similarity between genes is often the starting point for building gene regulatory networks. Most similarity measures used in practice only consider pairwise information with a few also consider network structure. Although theoretical properties of pairwise measures are well understood in the statistics literature, little is known about their statistical properties of those similarity measures based on network structure. In this article, we consider a new whole genome network-based similarity measure, called CCor, that makes use of information of all the genes in the network. We derive a concentration inequality of CCor and compare it with the commonly used Pearson correlation coefficient for inferring network modules. Both theoretical analysis and real data example demonstrate the advantages of CCor over existing measures for inferring gene modules.

Microarray Analysis of Rice d1 (RGA1) Mutant Reveals the Potential Role of G-Protein Alpha Subunit in Regulating Multiple Abiotic Stresses Such as Drought, Salinity, Heat, and Cold

The genome-wide role of heterotrimeric G-proteins in abiotic stress response in rice has not been examined from a functional genomics perspective, despite the availability of mutants and evidences involving individual genes/processes/stresses. Our rice whole transcriptome microarray analysis (GSE 20925 at NCBI GEO) using the G-alpha subunit (RGA1) null mutant (Daikoku 1 or d1) and its corresponding wild type (Oryza sativa Japonica Nipponbare) identified 2270 unique differentially expressed genes (DEGs). Out of them, we mined for all the potentially abiotic stress-responsive genes using Gene Ontology terms, STIFDB2.0 and Rice DB. The first two approaches produced smaller subsets of the 1886 genes found at Rice DB. The GO approach revealed similar regulation of several families of stress-responsive genes in RGA1 mutant. The Genevestigator analysis of the stress-responsive subset of the RGA1-regulated genes from STIFDB revealed cold and drought-responsive clusters. Meta data analysis at Rice DB revealed large stress-response categories such as cold (878 up/810 down), drought (882 up/837 down), heat (913 up/777 down), and salt stress (889 up/841 down). One thousand four hundred ninety-eight of them are common to all the four abiotic stresses, followed by fewer genes common to smaller groups of stresses. The RGA1-regulated genes that uniquely respond to individual stresses include 111 in heat stress, eight each in cold only and drought only stresses, and two genes in salt stress only. The common DEGs (1498) belong to pathways such as the synthesis of polyamine, glycine-betaine, proline, and trehalose. Some of the common DEGs belong to abiotic stress signaling pathways such as calcium-dependent pathway, ABA independent and dependent pathway, and MAP kinase pathway in the RGA1 mutant. Gene ontology of the common stress responsive DEGs revealed 62 unique molecular functions such as transporters, enzyme regulators, transferases, hydrolases, carbon and protein metabolism, binding to nucleotides, carbohydrates, receptors and lipids, morphogenesis, flower development, and cell homeostasis. We also mined 63 miRNAs that bind to the stress responsive transcripts identified in this study, indicating their post-transcriptional regulation. Overall, these results indicate the potentially extensive role of RGA1 in the regulation of multiple abiotic stresses in rice for further validation.

Biochemical and physiological processes associated with the differential ozone response in ozone-tolerant and sensitive soybean genotypes

Biochemical and physiological traits of two soybean [Glycine max (L.) Merr.] genotypes differing in sensitivity to ozone (O3 ) were investigated to determine the possible basis for the differential response. Fiskeby III (O3 -tolerant) and Mandarin (Ottawa) (O3 -sensitive) were grown in a greenhouse with charcoal-filtered air for 4 weeks, then treated with O3 for 7 h·day(-1) in greenhouse chambers. Mandarin (Ottawa) showed significantly more leaf injury and hydrogen peroxide (H2 O2 ) and superoxide (O2 (-) ) production compared with Fiskeby III. Peroxidase activity in Mandarin (Ottawa) was 31% higher with O3 but was not significantly different in Fiskeby III. Ozone did not affect superoxide dismutase or glutathione reductase activities, or leaf concentrations of glutathione or ascorbic acid. Thus, variation in O3 response between Fiskeby III and Mandarin (Ottawa) was not explained by differences in antioxidant enzymes and metabolites tested. Ethylene emission from leaves declined in Fiskeby III following O3 exposure but not in Mandarin (Ottawa). Ozone exposure reduced quantum yield (ΦPSII ), electron transport rate (ETR) and photochemical quenching (qp ) in Mandarin (Ottawa) more than in Fiskeby III, indicating that efficiency of energy conversion of PSII and photosynthetic electron transport was altered differently in the two genotypes. Short-term exposure to O3 had minimal effects on net carbon exchange rates of both soybean cultivars. A trend toward higher stomatal conductance in Mandarin (Ottawa) suggested stomatal exclusion might contribute to differential O3 sensitivity of the two genotypes. Increased sensitivity of Mandarin (Ottawa) to O3 was associated with higher H2 O2 and O2 (-) production compared with Fiskeby III, possibly associated with genotype differences in stomatal function or regulation of ethylene during the initial phases of O3 response.

G-protein α-subunit (GPA1) regulates stress, nitrate and phosphate response, flavonoid biosynthesis, fruit/seed development and substantially shares GCR1 regulation in A. thaliana

Heterotrimeric G-proteins are implicated in several plant processes, but the mechanisms of signal-response coupling and the roles of G-protein coupled receptors in general and GCR1 in particular, remain poorly understood. We isolated a knock-out mutant of the Arabidopsis G-protein α subunit (gpa1-5) and analysed its transcriptome to understand the genomewide role of GPA1 and compared it with that of our similar analysis of a GCR1 mutant (Chakraborty et al. 2015, PLoS ONE 10(2):e0117819). We found 394 GPA1-regulated genes spanning 79 biological processes, including biotic and abiotic stresses, development, flavonoid biosynthesis, transcription factors, transporters and nitrate/phosphate responses. Many of them are either unknown or unclaimed explicitly in other published gpa1 mutant transcriptome analyses. A comparison of all known GPA1-regulated genes (including the above 394) with 350 GCR1-regulated genes revealed 114 common genes. This can be best explained by GCR1-GPA1 coupling, or by convergence of their independent signaling pathways. Though the common genes in our GPA1 and GCR1 mutant datasets constitute only 26% of the GPA1-regulated and 30% of the GCR1-responsive genes, they belong to nearly half of all the processes affected in both the mutants. Thus, GCR1 and GPA1 regulate not only some common genes, but also different genes belonging to the same processes to achieve similar outcomes. Overall, we validate some known and report many hitherto unknown roles of GPA1 in plants, including agronomically important ones such as biotic stress and nutrient response, and also provide compelling genetic evidence to revisit the role of GCR1 in G-protein signalling.

G-protein Signaling Components GCR1 and GPA1 Mediate Responses to Multiple Abiotic Stresses in Arabidopsis

G-protein signaling components have been implicated in some individual stress responses in Arabidopsis, but have not been comprehensively evaluated at the genetic and biochemical level. Stress emerged as the largest functional category in our whole transcriptome analyses of knock-out mutants of GCR1 and/or GPA1 in Arabidopsis (Chakraborty et al., 2015a,b). This led us to ask whether G-protein signaling components offer converging points in the plant's response to multiple abiotic stresses. In order to test this hypothesis, we carried out detailed analysis of the abiotic stress category in the present study, which revealed 144 differentially expressed genes (DEGs), spanning a wide range of abiotic stresses, including heat, cold, salt, light stress etc. Only 10 of these DEGs are shared by all the three mutants, while the single mutants (GCR1/GPA1) shared more DEGs between themselves than with the double mutant (GCR1-GPA1). RT-qPCR validation of 28 of these genes spanning different stresses revealed identical regulation of the DEGs shared between the mutants. We also validated the effects of cold, heat and salt stresses in all the 3 mutants and WT on % germination, root and shoot length, relative water content, proline content, lipid peroxidation and activities of catalase, ascorbate peroxidase and superoxide dismutase. All the 3 mutants showed evidence of stress tolerance, especially to cold, followed by heat and salt, in terms of all the above parameters. This clearly shows the role of GCR1 and GPA1 in mediating the plant's response to multiple abiotic stresses for the first time, especially cold, heat and salt stresses. This also implies a role for classical G-protein signaling pathways in stress sensitivity in the normal plants of Arabidopsis. This is also the first genetic and biochemical evidence of abiotic stress tolerance rendered by knock-out mutation of GCR1 and/or GPA1. This suggests that G-protein signaling pathway could offer novel common targets for the development of tolerance/resistance to multiple abiotic stresses.

Cytoplasmic and Nuclear Localizations Are Important for the Hypersensitive Response Conferred by Maize Autoactive Rp1-D21 Protein

Disease resistance (R) genes have been isolated from many plant species. Most encode nucleotide binding leucine-rich repeat (NLR) proteins that trigger a rapid localized programmed cell death called the hypersensitive response (HR) upon pathogen recognition. Despite their structural similarities, different NLR are distributed in a range of subcellular locations, and analogous domains play diverse functional roles. The autoactive maize NLR gene Rp1-D21 derives from an intragenic recombination between two NLR genes, Rp1-D and Rp1-dp2, and confers a HR independent of the presence of a pathogen. Rp1-D21 and its N-terminal coiled coil (CC) domain (CCD21) confer autoactive HR when transiently expressed in Nicotiana benthamiana. Rp1-D21 was predominantly localized in cytoplasm with a small amount in the nucleus, while CCD21 was localized in both nucleus and cytoplasm. Targeting of Rp1-D21 or CCD21 predominantly to either the nucleus or the cytoplasm abolished HR-inducing activity. Coexpression of Rp1-D21 or CCD21 constructs confined, respectively, to the nucleus and cytoplasm did not rescue full activity, suggesting nucleocytoplasmic movement was important for HR induction. This work emphasizes the diverse structural and subcellular localization requirements for activity found among plant NLR R genes.

Abscisic acid affects transcription of chloroplast genes via protein phosphatase 2C-dependent activation of nuclear genes: repression by guanosine-3'-5'-bisdiphosphate and activation by sigma factor 5

Abscisic acid (ABA) represses the transcriptional activity of chloroplast genes (determined by run-on assays), with the exception of psbD and a few other genes in wild-type Arabidopsis seedlings and mature rosette leaves. Abscisic acid does not influence chloroplast transcription in the mutant lines abi1-1 and abi2-1 with constitutive protein phosphatase 2C (PP2C) activity, suggesting that ABA affects chloroplast gene activity by binding to the pyrabactin resistance (PYR)/PYR1-like or regulatory component of ABA receptor protein family (PYR/PYL/RCAR) and signaling via PP2Cs and sucrose non-fermenting protein-related kinases 2 (SnRK2s). Further we show by quantitative PCR that ABA enhances the transcript levels of RSH2, RSH3, PTF1 and SIG5. RelA/SpoT homolog 2 (RSH2) and RSH3 are known to synthesize guanosine-3'-5'-bisdiphosphate (ppGpp), an inhibitor of the plastid-gene-encoded chloroplast RNA polymerase. We propose, therefore, that ABA leads to an inhibition of chloroplast gene expression via stimulation of ppGpp synthesis. On the other hand, sigma factor 5 (SIG5) and plastid transcription factor 1 (PTF1) are known to be necessary for the transcription of psbD from a specific light- and stress-induced promoter (the blue light responsive promoter, BLRP). We demonstrate that ABA activates the psbD gene by stimulation of transcription initiation at BLRP. Taken together, our data suggest that ABA affects the transcription of chloroplast genes by a PP2C-dependent activation of nuclear genes encoding proteins involved in chloroplast transcription.

A cell type-specific view on the translation of mRNAs from ROS-responsive genes upon paraquat treatment of Arabidopsis thaliana leaves

Oxidative stress causes dramatic changes in the expression levels of many genes. The formation of a functional protein through successful mRNA translation is central to a coordinated cellular response. To what extent the response towards reactive oxygen species (ROS) is regulated at the translational level is poorly understood. Here we analysed leaf- and tissue-specific translatomes using a set of transgenic Arabidopsis thaliana lines expressing a FLAG-tagged ribosomal protein to immunopurify polysome-bound mRNAs before and after oxidative stress. We determined transcript levels of 171 ROS-responsive genes upon paraquat treatment, which causes formation of superoxide radicals, at the whole-organ level. Furthermore, the translation of mRNAs was determined for five cell types: mesophyll, bundle sheath, phloem companion, epidermal and guard cells. Mesophyll and bundle sheath cells showed the strongest response to paraquat treatment. Interestingly, several ROS-responsive transcription factors displayed cell type-specific translation patterns, while others were translated in all cell types. In part, cell type-specific translation could be explained by the length of the 5'-untranslated region (5'-UTR) and the presence of upstream open reading frames (uORFs). Our analysis reveals insights into the translational regulation of ROS-responsive genes, which is important to understanding cell-specific responses and functions during oxidative stress.

Plant signalling in acute ozone exposure

Exposure of plants to high ozone concentrations causes lesion formation in sensitive plants. Plant responses to ozone involve fast and massive changes in protein activities, gene expression and metabolism even before any tissue damage can be detected. Degradation of ozone and subsequent accumulation of reactive oxygen species (ROS) in the extracellular space activates several signalling cascades, which are integrated inside the cell into a fine-balanced network of ROS signalling. Reversible protein phosphorylation and degradation plays an important role in the regulation of signalling mechanisms in a complex crosstalk with plant hormones and calcium, an essential second messenger. In this review, we discuss the recent advances in understanding the molecular mechanisms of ozone uptake, perception and signalling pathways activated during the early steps of ozone response, and discuss the use of ozone as a tool to study the function of apoplastic ROS in signalling.

Insights into the mechanism of cell death induced by saporin delivered into cancer cells by an antibody fusion protein targeting the transferrin receptor 1

We previously developed an antibody-avidin fusion protein (ch128.1Av) that targets the human transferrin receptor 1 (TfR1) and exhibits direct cytotoxicity against malignant B cells in an iron-dependent manner. ch128.1Av is also a delivery system and its conjugation with biotinylated saporin (b-SO6), a plant ribosome-inactivating toxin, results in a dramatic iron-independent cytotoxicity, both in malignant cells that are sensitive or resistant to ch128.1Av alone, in which the toxin effectively inhibits protein synthesis and triggers caspase activation. We have now found that the ch128.1Av/b-SO6 complex induces a transcriptional response consistent with oxidative stress and DNA damage, a response that is not observed with ch128.1Av alone. Furthermore, we show that the antioxidant N-acetylcysteine partially blocks saporin-induced apoptosis suggesting that oxidative stress contributes to DNA damage and ultimately saporin-induced cell death. Interestingly, the toxin was detected in nuclear extracts by immunoblotting, suggesting the possibility that saporin might induce direct DNA damage. However, confocal microscopy did not show a clear and consistent pattern of intranuclear localization. Finally, using the long-term culture-initiating cell assay we found that ch128.1Av/b-SO6 is not toxic to normal human hematopoietic stem cells suggesting that this critical cell population would be preserved in therapeutic interventions using this immunotoxin.

Re-evaluating the role of ascorbic acid and phenolic glycosides in ozone scavenging in the leaf apoplast of Arabidopsis thaliana L

Phenolic glycosides are effective reactive oxygen scavengers and peroxidase substrates, suggesting that compounds in addition to ascorbate may have functional importance in defence responses against ozone (O(3)), especially in the leaf apoplast. The apoplastic concentrations of ascorbic acid (AA) and phenolic glycosides in Arabidopsis thaliana L. Col-0 wild-type plants were determined following exposure to a range of O(3) concentrations (5, 125 or 175 nL L(-1)) in controlled environment chambers. AA in leaf apoplast extracts was almost entirely oxidized in all treatments, suggesting that O(3) scavenging by direct reactions with reduced AA was very limited. In regard to phenolics, O(3) stimulated transcription of numerous phenylpropanoid pathway genes and increased the apoplastic concentration of sinapoyl malate. However, modelling of O(3) scavenging in the apoplast indicated that sinapoyl malate concentrations were too low to be effective protectants. Furthermore, null mutants for sinapoyl esters (fah1-7), kaempferol glycosides (tt4-1) and the double mutant (tt4-1/fah1-7) were equally sensitive to chronic O(3) as Ler-0 wild-type plants. These results indicate that current understanding of O(3) defence schemes deserves reassessment as mechanisms other than direct scavenging of O(3) by extracellular AA and antioxidant activity of some phenolics may predominate in some plant species.

Dissecting Arabidopsis Gβ signal transduction on the protein surface

The heterotrimeric G-protein complex provides signal amplification and target specificity. The Arabidopsis (Arabidopsis thaliana) Gβ-subunit of this complex (AGB1) interacts with and modulates the activity of target cytoplasmic proteins. This specificity resides in the structure of the interface between AGB1 and its targets. Important surface residues of AGB1, which were deduced from a comparative evolutionary approach, were mutated to dissect AGB1-dependent physiological functions. Analysis of the capacity of these mutants to complement well-established phenotypes of Gβ-null mutants revealed AGB1 residues critical for specific AGB1-mediated biological processes, including growth architecture, pathogen resistance, stomata-mediated leaf-air gas exchange, and possibly photosynthesis. These findings provide promising new avenues to direct the finely tuned engineering of crop yield and traits.