Effects of chronic ozone exposure on gene expression in Arabidopsis thaliana ecotypes and in Thellungiella halophila

Adaptative Mechanisms of Halophytic Eutrema salsugineum Encountering Saline Environment

Salt cress (Eutrema salsugineum), an Arabidopsis-related halophyte, can naturally adapt to various harsh climates and soil conditions; thus, it is considered a desirable model plant for deciphering mechanisms of salt and other abiotic stresses. Accumulating evidence has revealed that compared with Arabidopsis, salt cress possesses stomata that close more tightly and more succulent leaves during extreme salt stress, a noticeably higher level of proline, inositols, sugars, and organic acids, as well as stress-associated transcripts in unstressed plants, and they are induced rapidly under stress. In this review, we systematically summarize the research on the morphology, physiology, genome, gene expression and regulation, and protein and metabolite profile of salt cress under salt stress. We emphasize the latest advances in research on the genome adaptive evolution encountering saline environments, and epigenetic regulation, and discuss the mechanisms underlying salt tolerance in salt cress. Finally, we discuss the existing questions and opportunities for future research in halophytic Eutrema. Together, the review fosters a better understanding of the mechanism of plant salt tolerance and provides a reference for the research and utilization of Eutrema as a model extremophile in the future. Furthermore, the prospects for salt cress applied to explore the mechanism of salt tolerance provide a theoretical basis to develop new strategies for agricultural biotechnology.

KLU/CYP78A5, a Cytochrome P450 Monooxygenase Identified via Fox Hunting, Contributes to Cuticle Biosynthesis and Improves Various Abiotic Stress Tolerances

Acquired osmotolerance after salt stress is widespread among Arabidopsis thaliana (Arabidopsis) accessions. Most salt-tolerant accessions exhibit acquired osmotolerance, whereas Col-0 does not. To identify genes that can confer acquired osmotolerance to Col-0 plants, we performed full-length cDNA overexpression (FOX) hunting using full-length cDNAs of halophyte Eutrema salsugineum, a close relative of Arabidopsis. We identified EsCYP78A5 as a gene that can confer acquired osmotolerance to Col-0 wild-type (WT) plants. EsCYP78A5 encodes a cytochrome P450 monooxygenase and the Arabidopsis ortholog is known as KLU. We also demonstrated that transgenic Col-0 plants overexpressing AtKLU (AtKLUox) exhibited acquired osmotolerance. Interestingly, KLU overexpression improved not only acquired osmotolerance but also osmo-shock, salt-shock, oxidative, and heat-stress tolerances. Under normal conditions, the AtKLUox plants showed growth retardation with shiny green leaves. The AtKLUox plants also accumulated higher anthocyanin levels and developed denser cuticular wax than WT plants. Compared to WT plants, the AtKLUox plants accumulated significantly higher levels of cutin monomers and very-long-chain fatty acids, which play an important role in the development of cuticular wax and membrane lipids. Endoplasmic reticulum (ER) stress induced by osmotic or heat stress was reduced in AtKLUox plants compared to WT plants. These findings suggest that KLU is involved in the cuticle biosynthesis, accumulation of cuticular wax, and reduction of ER stress induced by abiotic stresses, leading to the observed abiotic stress tolerances.

Dissecting the Molecular Regulation of Natural Variation in Growth and Senescence of Two Eutrema salsugineum Ecotypes

Salt cress (Eutrema salsugineum, aka Thellungiella salsuginea) is an extremophile and a close relative of Arabidopsis thaliana. To understand the mechanism of selection of complex traits under natural variation, we analyzed the physiological and proteomic differences between Shandong (SD) and Xinjiang (XJ) ecotypes. The SD ecotype has dark green leaves, short and flat leaves, and more conspicuous taproots, and the XJ ecotype had greater biomass and showed clear signs of senescence or leaf shedding with age. After 2-DE separation and ESI-MS/MS identification, between 25 and 28 differentially expressed protein spots were identified in shoots and roots, respectively. The proteins identified in shoots are mainly involved in cellular metabolic processes, stress responses, responses to abiotic stimuli, and aging responses, while those identified in roots are mainly involved in small-molecule metabolic processes, oxidation-reduction processes, and responses to abiotic stimuli. Our data revealed the evolutionary differences at the protein level between these two ecotypes. Namely, in the evolution of salt tolerance, the SD ecotype highly expressed some stress-related proteins to structurally adapt to the high salt environment in the Yellow River Delta, whereas the XJ ecotype utilizes the specialized energy metabolism to support this evolution of the short-lived xerophytes in the Xinjiang region.

Genomics and Pathways Involved in Maize Resistance to Fusarium Ear Rot and Kernel Contamination With Fumonisins

Fusarium verticillioides is a causal agent of maize ear rot and produces fumonisins, which are mycotoxins that are toxic to animals and humans. In this study, quantitative trait loci (QTLs) and bulk-segregant RNA-seq approaches were used to uncover genomic regions and pathways involved in resistance to Fusarium ear rot (FER) and to fumonisin accumulation in maize kernels. Genomic regions at bins 4.07-4.1, 6-6.01, 6.04-6.05, and 8.05-8.08 were related to FER resistance and/or reduced fumonisin levels in kernels. A comparison of transcriptomes between resistant and susceptible inbred bulks 10 days after inoculation with F. verticillioides revealed 364 differentially expressed genes (DEGs). In the resistant inbred bulks, genes involved in sink metabolic processes such as fatty acid and starch biosynthesis were downregulated, as well as those involved in phytosulfokine signaling and many other genes involved in cell division; while genes involved in secondary metabolism and compounds/processes related to resistance were upregulated, especially those related to cell wall biosynthesis/rearrangement and flavonoid biosynthesis. These trends are indicative of a growth-defense trade-off. Among the DEGs, Zm00001d053603, Zm00001d035562, Zm00001d037810, Zm00001d037921, and Zm00001d010840 were polymorphic between resistant and susceptible bulks, were located in the confidence intervals of detected QTLs, and showed large differences in transcript levels between the resistant and susceptible bulks. Thus, they were identified as candidate genes involved in resistance to FER and/or reduced fumonisin accumulation.

Transcriptome Profiling of the Salt Stress Response in the Leaves and Roots of Halophytic Eutrema salsugineum

Eutrema salsugineum can grow in natural harsh environments; however, the underlying mechanisms for salt tolerance of Eutrema need to be further understood. Herein, the transcriptome profiling of Eutrema leaves and roots exposed to 300 mM NaCl is investigated, and the result emphasized the role of genes involved in lignin biosynthesis, autophagy, peroxisome, and sugar metabolism upon salt stress. Furthermore, the expression of the lignin biosynthesis and autophagy-related genes, as well as 16 random selected genes, was validated by qRT-PCR. Notably, the transcript abundance of a large number of lignin biosynthesis genes such as CCoAOMT, C4H, CCR, CAD, POD, and C3′H in leaves was markedly elevated by salt shock. And the examined lignin content in leaves and roots demonstrated salt stress led to lignin accumulation, which indicated the enhanced lignin level could be an important mechanism for Eutrema responding to salt stress. Additionally, the differentially expressed genes (DEGs) assigned in the autophagy pathway including Vac8, Atg8, and Atg4, as well as DEGs enriched in the peroxisome pathway such as EsPEX7, EsCAT, and EsSOD2, were markedly induced in leaves and/or roots. In sugar metabolism pathways, the transcript levels of most DEGs associated with the synthesis of sucrose, trehalose, raffinose, and xylose were significantly enhanced. Furthermore, the expression of various stress-related transcription factor genes including WRKY, AP2/ERF-ERF, NAC, bZIP, MYB, C2H2, and HSF was strikingly improved. Collectively, the increased expression of biosynthesis genes of lignin and soluble sugars, as well as the genes in the autophagy and peroxisome pathways, suggested that Eutrema encountering salt shock possibly possess a higher capacity to adjust osmotically and facilitate water transport and scavenge reactive oxidative species and oxidative proteins to cope with the salt environment. Thus, this study provides a new insight for exploring the salt tolerance mechanism of halophytic Eutrema and discovering new gene targets for the genetic improvement of crops.

Ozone Induced Stomatal Regulations, MAPK and Phytohormone Signaling in Plants

Ozone (O₃) is a gaseous environmental pollutant that can enter leaves through stomatal pores and cause damage to foliage. It can induce oxidative stress through the generation of reactive oxygen species (ROS) like hydrogen peroxide (H₂O₂) that can actively participate in stomatal closing or opening in plants. A number of phytohormones, including abscisic acid (ABA), ethylene (ET), salicylic acid (SA), and jasmonic acid (JA) are involved in stomatal regulation in plants. The effects of ozone on these phytohormones’ ability to regulate the guard cells of stomata have been little studied, however, and the goal of this paper is to explore and understand the effects of ozone on stomatal regulation through guard cell signaling by phytohormones. In this review, we updated the existing knowledge by considering several physiological mechanisms related to stomatal regulation after response to ozone. The collected information should deepen our understanding of the molecular pathways associated with response to ozone stress, in particular, how it influences stomatal regulation, mitogen-activated protein kinase (MAPK) activity, and phytohormone signaling. After summarizing the findings and noting the gaps in the literature, we present some ideas for future research on ozone stress in plants

Network Analysis of Local Gene Regulators in Arabidopsis thaliana under Spaceflight Stress

Spaceflight microgravity affects normal plant growth in several ways. The transcriptional dataset of the plant model organism Arabidopsis thaliana grown in the international space station is mined using graph-theoretic network analysis approaches to identify significant gene transcriptions in microgravity essential for the plant’s survival and growth in altered environments. The photosynthesis process is critical for the survival of the plants in spaceflight under different environmentally stressful conditions such as lower levels of gravity, lesser oxygen availability, low atmospheric pressure, and the presence of cosmic radiation. Lasso regression method is used for gene regulatory network inferencing from gene expressions of four different ecotypes of Arabidopsis in spaceflight microgravity related to the photosynthetic process. The individual behavior of hub-genes and stress response genes in the photosynthetic process and their impact on the whole network is analyzed. Logistic regression on centrality measures computed from the networks, including average shortest path, betweenness centrality, closeness centrality, and eccentricity, and the HITS algorithm is used to rank genes and identify interactor or target genes from the networks. Through the hub and authority gene interactions, several biological processes associated with photosynthesis and carbon fixation genes are identified. The altered conditions in spaceflight have made all the ecotypes of Arabidopsis sensitive to dehydration-and-salt stress. The oxidative and heat-shock stress-response genes regulate the photosynthesis genes that are involved in the oxidation-reduction process in spaceflight microgravity, enabling the plant to adapt successfully to the spaceflight environment.

Evidence of Ozone-Induced Visible Foliar Injury in Hong Kong Using Phaseolus Vulgaris as a Bioindicator

(1) Background: Hong Kong is one of the most densely populated cities in the world, with millions of people exposed to severe air pollution. Surface ozone, mostly produced photochemically from anthropogenic precursor gases, is harmful to both humans and vegetation. The phytotoxicity of ozone has been shown to damage plant photosynthesis, induce early leaf death, and retard growth. (2) Methods: We use genotypes of bush bean Phaseolus vulgaris with various degrees of sensitivity to ozone to investigate the impacts of ambient ozone on the morphology and development of the beans. We use ozone-induced foliar injury index and measure the flowering and fruit production to quantify the ozone stress on the plants. (3) Results: We expected that the ozone-sensitive genotype would suffer from a reduction of yield. Results, however, show that the ozone-sensitive genotype suffers higher ozone-induced foliar damage as expected but produces more pods and beans and heavier beans than the ozone-resistant genotype. (4) Conclusions: It is postulated that the high ozone sensitivity of the sensitive genotype causes stress-induced flowering, and therefore results in higher bean yield. A higher than ambient concentration of ozone is needed to negatively impact the yield production of the ozone-sensitive genotype. Meanwhile, ozone-induced foliar damage shows a graduated scale of damage pattern that can be useful for indicating ozone levels. This study demonstrates the usefulness of bioindicators to monitor the phytotoxic effects of ozone pollution in a subtropical city such as Hong Kong.

Ozone treatments activate defence responses against Meloidogyne incognita and Tomato spotted wilt virus in tomato

BACKGROUND

Ozonated water (O₃ wat) soil drench and/or foliar spray applications were evaluated for their potential to control the root-knot nematode Meloidogyne incognita (RKN) and the airborne pathogen Tomato spotted wilt virus (TSWV) in tomato. We investigated how O₃ wat modulates the salicylic acid/jasmonic acid/ethylene (SA/JA/ET) signalling network in the host, locally and systemically, to induce resistance to nematode and virus.

RESULTS

The application as soil drench was effective in reducing the number of galls and egg masses, but did not reduce the incidence and severity of TSWV infection. Conversely, O₃ wat applied by foliar spray decreased TSWV disease incidence and severity (-20%), but was not able to control M. incognita infection. SA-related genes were generally upregulated in both locally treated and systemically reached tissues, showing a positive action of the O₃ wat treatment on SA signalling. Neither O₃ wat application method significantly altered JA-related gene expression in either direction. ET-related genes were differentially regulated by root or leaf treatments, indicating that O₃ wat may have different effects on ET-mediated signalling in different organs. JA/ET/SA related pathways were differentially modulated by O₃ wat in the presence of either RKN or TSWV.

CONCLUSION

O₃ wat had a higher efficacy when applied directly to organs challenged by the pathogens, although it was potentially able to stimulate defence responses through the activation of SA signalling. Owing to its safety and effectiveness in controlling nematode and virus infections, O₃ wat can be considered as a possible alternative tool for sustainable disease management practices. © 2019 Society of Chemical Industry.

A member of the CONSTANS-Like protein family is a putative regulator of reactive oxygen species homeostasis and spaceflight physiological adaptation

A feature of the physiological adaptation to spaceflight in Arabidopsis thaliana (Arabidopsis) is the induction of reactive oxygen species (ROS)-associated gene expression. The patterns of ROS-associated gene expression vary among Arabidopsis ecotypes, and the role of ROS signalling in spaceflight acclimation is unknown. What could differences in ROS gene regulation between ecotypes on orbit reveal about physiological adaptation to novel environments? Analyses of ecotype-dependent responses to spaceflight resulted in the elucidation of a previously uncharacterized gene (OMG1) as being ROS-associated. The OMG1 5' flanking region is an active promoter in cells where ROS activity is commonly observed, such as in pollen tubes, root hairs, and in other tissues upon wounding. qRT-PCR analyses revealed that upon wounding on Earth, OMG1 is an apparent transcriptional regulator of MYB77 and GRX480, which are associated with the ROS pathway. Fluorescence-based ROS assays show that OMG1 affects ROS production. Phylogenetic analysis of OMG1 and closely related homologs suggests that OMG1 is a distant, unrecognized member of the CONSTANS-Like protein family, a member that arose via gene duplication early in the angiosperm lineage and subsequently lost its first DNA-binding B-box1 domain. These data illustrate that members of the rapidly evolving COL protein family play a role in regulating ROS pathway functions, and their differential regulation on orbit suggests a role for ROS signalling in spaceflight physiological adaptation.

Does ozone increase ABA levels by non-enzymatic synthesis causing stomata to close?

Reactive oxygen species (ROS) are widely recognized as important regulators of stomatal aperture and plant gas exchange. The pathways through which stomata perceive ROS share many common linkages with the well characterized signalling pathway for the hormone abscisic acid (ABA), a major driver of stomatal closure. Given reports that ABA receptor mutants have no stomatal response to ozone-triggered ROS production, as well as evidence that all steps in the ABA biosynthetic pathway can be non-enzymatically converted by ROS, here we investigated the possibility that ozone closes stomata by directly converting ABA precursors to ABA. In plants where stomata were responsive to ozone, we found that foliar ABA levels rapidly increased upon exposure to ozone. Recovery of gas exchange post-exposure occurred only when ABA levels declined. Our data suggest that stomatal closure in response to ozone exposure occurs as a result of direct oxidation of ABA precursors leading to ABA production, but the importance of this ROS interaction remains uncertain under normal photosynthetic conditions.

A Different Pattern of Production and Scavenging of Reactive Oxygen Species in Halophytic Eutrema salsugineum (Thellungiella salsuginea) Plants in Comparison to Arabidopsis thaliana and Its Relation to Salt Stress Signaling

Isolated thylakoids from halophytic Eutrema salsugineum (Thellungiella salsuginea) produces more H2O2 in comparison to glycophytic Arabidopsis thaliana. The first objective of this study was to verify whether this feature is relevant also to the intact chloroplasts and leaves. Enhanced H2O2 levels in chloroplasts and leaves of E. salsugineum were positively verified with several methods (electron microscopy, staining with Amplex Red and with diaminobenzidine). This effect was associated with a decreased ratio of [Formula: see text]/H2O2 in E. salsugineum in comparison to A. thaliana as detected by electron paramagnetic resonance method. As a next step, we tested how this specific ROS signature of halophytic species affects the antioxidant status and down-stream components of ROS signaling. Comparison of enzymatic antioxidants revealed a decreased activity of ascorbate peroxidase (APX), enhanced activity of glutathione peroxidase, and the presence of thylakoid-bound forms of iron superoxide dismutase (FeSOD) and APX in E. salsugineum. These cues were, however, independent from application of salt stress. The typical H2O2-dependent cellular responses, namely the levels of glucosinolates and stress-related hormones were determined. The total glucosinolate content in E. salsugineum water-treated leaves was higher than in A. thaliana and increased after salinity treatment. Treatment with salinity up-regulated all of tested stress hormones, their precursors and catabolites [abscisic acid (ABA), dihydrophaseic acid, phaseic acid, 1-aminocyclopropane-1-carboxylic acid, salicylic acid, jasmonic acid, cis-(+)-12-oxo-phytodienoic acid and jasmonoyl-L-isoleucine] in A. thaliana, whereas in E. salsugineum only a stimulation in ethylene synthesis and ABA catabolism was noted. Obtained results suggest that constitutively enhanced H2O2 generation in chloroplasts of E. salsugineum might be a crucial component of stress-prepardeness of this halophytic species. It shapes a very efficient antioxidant protection (in which glucosinolates might play a specific role) and a fine tuning of hormonal signaling to suppress the cell death program directed by jasmonate pathway.

Transcriptomics and functional genomics of ROS-induced cell death regulation by RADICAL-INDUCED CELL DEATH1

Plant responses to changes in environmental conditions are mediated by a network of signaling events leading to downstream responses, including changes in gene expression and activation of cell death programs. Arabidopsis thaliana RADICAL-INDUCED CELL DEATH1 (RCD1) has been proposed to regulate plant stress responses by protein-protein interactions with transcription factors. Furthermore, the rcd1 mutant has defective control of cell death in response to apoplastic reactive oxygen species (ROS). Combining transcriptomic and functional genomics approaches we first used microarray analysis in a time series to study changes in gene expression after apoplastic ROS treatment in rcd1. To identify a core set of cell death regulated genes, RCD1-regulated genes were clustered together with other array experiments from plants undergoing cell death or treated with various pathogens, plant hormones or other chemicals. Subsequently, selected rcd1 double mutants were constructed to further define the genetic requirements for the execution of apoplastic ROS induced cell death. Through the genetic analysis we identified WRKY70 and SGT1b as cell death regulators functioning downstream of RCD1 and show that quantitative rather than qualitative differences in gene expression related to cell death appeared to better explain the outcome. Allocation of plant energy to defenses diverts resources from growth. Recently, a plant response termed stress-induced morphogenic response (SIMR) was proposed to regulate the balance between defense and growth. Using a rcd1 double mutant collection we show that SIMR is mostly independent of the classical plant defense signaling pathways and that the redox balance is involved in development of SIMR.

Reactive oxygen species (ROS) are utilized in plants as signaling molecules to regulate development, stress responses and cell death. One extreme form of defense uses programmed cell death (PCD) in a scorched earth strategy to deliberately kill off cells invaded by a pathogen. Compared to animals, the regulation of plant PCD remains largely uncharacterized, particularly with regard to how ROS regulate changes in gene expression leading to PCD. Using comparative transcriptome analysis of mutants deficient in PCD regulation and publicly available cell death microarray data, we show that quantitative rather than qualitative differences in cell death gene expression appear to better explain the cell death response. In a genetic analysis with double mutants we also found the transcription factor WRKY70 and a component of ubiquitin mediated protein degradation, SGT1b, to be involved in regulation of ROS induced PCD.

Plant chemical defense allocation constrains evolution of tolerance to community change across a range boundary

Because transplant experiments show that performance usually decreases across species range boundaries, some range limits might develop from factors and processes that prevent adaptation to stressful environments. Here, we determined whether an ecological cost of plant defense involving stress associated with changes in the local plant community may contribute to range limit development in the upland mustard species Boechera stricta. In a common garden experiment of 499 B. stricta plants, performance decreased and a multivariate axis of community structure increased across the boundary, indicating increased stress associated with the community change. There was also significant genetic variation (evolutionary potential) among marker-inferred inbred lines of B. stricta for tolerance to the stress; however, lines with high basal levels of glucosinolate toxins had lower tolerance to the change in community structure. We suggest that defense allocation, which is also needed across the range, may impede adaptation to the stress associated with the community change and thus contribute to range limit development.

Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum)

Background

Most molecular studies of plant stress tolerance have been performed with Arabidopsis thaliana, although it is not particularly stress tolerant and may lack protective mechanisms required to survive extreme environmental conditions. Thellungiella salsuginea has attracted interest as an alternative plant model species with high tolerance of various abiotic stresses. While the T. salsuginea genome has recently been sequenced, its annotation is still incomplete and transcriptomic information is scarce. In addition, functional genomics investigations in this species are severely hampered by a lack of affordable tools for genome-wide gene expression studies.

Results

Here, we report the results of Thellungiella de novo transcriptome assembly and annotation based on 454 pyrosequencing and development and validation of a T. salsuginea microarray. ESTs were generated from a non-normalized and a normalized library synthesized from RNA pooled from samples covering different tissues and abiotic stress conditions. Both libraries yielded partially unique sequences, indicating their necessity to obtain comprehensive transcriptome coverage. More than 1 million sequence reads were assembled into 42,810 unigenes, approximately 50% of which could be functionally annotated. These unigenes were compared to all available Thellungiella genome sequence information. In addition, the groups of Late Embryogenesis Abundant (LEA) proteins, Mitogen Activated Protein (MAP) kinases and protein phosphatases were annotated in detail. We also predicted the target genes for 384 putative miRNAs. From the sequence information, we constructed a 44 k Agilent oligonucleotide microarray. Comparison of same-species and cross-species hybridization results showed superior performance of the newly designed array for T. salsuginea samples. The developed microarrays were used to investigate transcriptional responses of T. salsuginea and Arabidopsis during cold acclimation using the MapMan software.

Conclusions

This study provides the first comprehensive transcriptome information for the extremophile Arabidopsis relative T. salsuginea. The data constitute a more than three-fold increase in the number of publicly available unigene sequences and will greatly facilitate genome annotation. In addition, we have designed and validated the first genome-wide microarray for T. salsuginea, which will be commercially available. Together with the publicly available MapMan software this will become an important tool for functional genomics of plant stress tolerance.

HsfA1d, a protein identified via FOX hunting using Thellungiella salsuginea cDNAs improves heat tolerance by regulating heat-stress-responsive gene expression

Thellungiella salsuginea (formerly T. halophila), a species closely related to Arabidopsis (Arabidopsis thaliana), is tolerant not only to high salt levels, but also to chilling, freezing, and ozone. Here, we report that T. salsuginea also shows greater heat tolerance than Arabidopsis. We identified T. salsuginea HsfA1d (TsHsfA1d) as a gene that can confer marked heat tolerance on Arabidopsis. TsHsfA1d was identified via Full-length cDNA Over-eXpressing gene (FOX) hunting from among a collection of heat-stress-related T. salsuginea cDNAs. Transgenic Arabidopsis overexpressing TsHsfA1d showed constitutive up-regulation of many genes in the Arabidopsis AtHsfA1 regulon under normal growth temperature. In Arabidopsis mesophyll protoplasts, TsHsfA1d was localized in both the nucleus and the cytoplasm. TsHsfA1d also interacted with AtHSP90, which negatively regulates AtHsfA1s by forming HsfA1-HSP90 complexes in the cytoplasm. It is likely that the partial nuclear localization of TsHsfA1d induced the expression of the AtHsfA1d regulon in the transgenic plants at normal temperature. We also discovered that transgenic Arabidopsis plants overexpressing AtHsfA1d were more heat-tolerant than wild-type plants and up-regulated the expression of the HsfA1d regulon, as was observed in TsHsfA1d-overexpressing plants. We propose that the products of both TsHsfA1d and AtHsfA1d function as positive regulators of Arabidopsis heat-stress response and would be useful for the improvement of heat-stress tolerance in other plants.

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.

The effects of tropospheric ozone on net primary productivity and implications for climate change

Tropospheric ozone (O(3)) is a global air pollutant that causes billions of dollars in lost plant productivity annually. It is an important anthropogenic greenhouse gas, and as a secondary air pollutant, it is present at high concentrations in rural areas far from industrial sources. It also reduces plant productivity by entering leaves through the stomata, generating other reactive oxygen species and causing oxidative stress, which in turn decreases photosynthesis, plant growth, and biomass accumulation. The deposition of O(3) into vegetation through stomata is an important sink for tropospheric O(3), but this sink is modified by other aspects of environmental change, including rising atmospheric carbon dioxide concentrations, rising temperature, altered precipitation, and nitrogen availability. We review the atmospheric chemistry governing tropospheric O(3) mass balance, the effects of O(3) on stomatal conductance and net primary productivity, and implications for agriculture, carbon sequestration, and climate change.

Apoplastic reactive oxygen species transiently decrease auxin signaling and cause stress-induced morphogenic response in Arabidopsis

Reactive oxygen species (ROS) are ubiquitous signaling molecules in plant stress and development. To gain further insight into the plant transcriptional response to apoplastic ROS, the phytotoxic atmospheric pollutant ozone was used as a model ROS inducer in Arabidopsis (Arabidopsis thaliana) and gene expression was analyzed with microarrays. In contrast to the increase in signaling via the stress hormones salicylic acid, abscisic acid, jasmonic acid (JA), and ethylene, ROS treatment caused auxin signaling to be transiently suppressed, which was confirmed with a DR5-uidA auxin reporter construct. Transcriptomic data revealed that various aspects of auxin homeostasis and signaling were modified by apoplastic ROS. Furthermore, a detailed analysis of auxin signaling showed that transcripts of several auxin receptors and Auxin/Indole-3-Acetic Acid (Aux/IAA) transcriptional repressors were reduced in response to apoplastic ROS. The ROS-derived changes in the expression of auxin signaling genes partially overlapped with abiotic stress, pathogen responses, and salicylic acid signaling. Several mechanisms known to suppress auxin signaling during biotic stress were excluded, indicating that ROS regulated auxin responses via a novel mechanism. Using mutants defective in various auxin (axr1, nit1, aux1, tir1 afb2, iaa28-1, iaa28-2) and JA (axr1, coi1-16) responses, ROS-induced cell death was found to be regulated by JA but not by auxin. Chronic ROS treatment resulted in altered leaf morphology, a stress response known as "stress-induced morphogenic response." Altered leaf shape of tir1 afb2 suggests that auxin was a negative regulator of stress-induced morphogenic response in the rosette.

Detecting functional groups of Arabidopsis mutants by metabolic profiling and evaluation of pleiotropic responses

Metabolic profiles and fingerprints of Arabidopsis thaliana plants with various defects in plastidic sugar metabolism or photosynthesis were analyzed to elucidate if the genetic mutations can be traced by comparing their metabolic status. Using a platform of chromatographic and spectrometric tools data from untargeted full MS scans as well as from selected metabolites including major carbohydrates, phosphorylated intermediates, carboxylates, free amino acids, major antioxidants, and plastidic pigments were evaluated. Our key observations are that by multivariate statistical analysis each mutant can be separated by a unique metabolic signature. Closely related mutants come close. Thus metabolic profiles of sugar mutants are different but more similar than those of photosynthesis mutants. All mutants show pleiotropic responses mirrored in their metabolic status. These pleiotropic responses are typical and can be used for separating and grouping of the mutants. Our findings show that metabolite fingerprints can be taken to classify mutants and hence may be used to sort genes into functional groups.

The physiological, transcriptional and genetic responses of an ozone-sensitive and an ozone tolerant poplar and selected extremes of their F2 progeny

Relatively little is known about the transcriptional response or genetic control of response and adaptation of trees to tropospheric ozone exposure. Such understanding is needed as up to 50% of forests, globally, may be subjected to phytotoxic concentrations of ozone. The physiological, transcriptional and genetic response to ozone was examined in Populus trichocarpa and P. deltoides, which show extreme sensitivity and tolerance to ozone, respectively. Using an inbred F2 mapping population derived from these two species, we mapped quantitative trait loci (QTL) for traits associated with ozone response, examined segregation of the transcriptional response to ozone and co-located genes showing divergent responses between tolerant and sensitive genotypes with QTL. QTL were identified linking detrimental effects of ozone with leaf and biomass traits and differential responses were found for key genes involved in ethylene production and response.

Differential gene expression in senescing leaves of two silver birch genotypes in response to elevated CO2 and tropospheric ozone

Long-term effects of elevated CO(2) and O(3) concentrations on gene expression in silver birch (Betula pendula Roth) leaves were studied during the end of the growing season. Two birch genotypes, clones 4 and 80, with different ozone growth responses, were exposed to 2x ambient CO(2) and/or O(3) in open-top chambers (OTCs). Microarray analyses were performed after 2 years of exposure, and the transcriptional profiles were compared to key physiological characteristics during leaf senescence. There were genotypic differences in the responses to CO(2) and O(3). Clone 80 exhibited greater transcriptional response and capacity to alter metabolism, resulting in better stress tolerance. The gene expression patterns of birch leaves indicated contrasting responses of senescence-related genes to elevated CO(2) and O(3). Elevated CO(2) delayed leaf senescence and reduced associated transcriptional changes, whereas elevated O(3) advanced leaf senescence because of increased oxidative stress. The combined treatment demonstrated that elevated CO(2) only temporarily alleviated the negative effects of O(3). Gene expression data alone were insufficient to explain the O(3) response in birch, and additional physiological and biochemical data were required to understand the true O(3) sensitivity of these clones.

No interaction between methyl jasmonate and ozone in Pima cotton: growth and allocation respond independently to both

Ozone (O3) is damaging to plants, inducing signalling pathways involving antagonism between jasmonates and ethylene. These pathways mediate O3 responses, particularly to acute exposure, and their manipulation protected several species against acute and chronic O3. We use chronic daily exposure of up to 163 ppb O3, and twice weekly application of up to 320 microg plant(-1) methyl jasmonate (MeJA) to test two hypothesizes: 1) a low rate of MeJA does not affect growth but increases O3 sensitivity; 2) a high rate inhibits growth but reduces O3 sensitivity. Both hypotheses were rejected. Growth declined with increases in both MeJA and O3. MeJA at 40 microg plant(-1) caused no direct effect, and at 160 microg plant(-1) reduced growth similarly at all O3. Neither rate altered O3 sensitivity. These additive responses are not consistent with protection by MeJA in this system. They may reflect inter-specific differences in signalling, since O3 concentrations used here exceeded some reported acute exposures. Alternatively, parallel responses to O3 and MeJA may suggest that O3-induced jasmonates play a developmental role in chronic response but no protective role in the absence of lesions characteristic of acute exposure. MeJA appears useful as a probe of these mechanisms.

Transcriptional signatures in leaves of adult European beech trees (Fagus sylvatica L.) in an experimentally enhanced free air ozone setting

Tropospheric ozone causes severe oxidative stress in plants. To investigate the transcriptional responsiveness of adult trees to ozone, fully-expanded sun and shade leaves of mature beech trees were harvested at four time points over the entire vegetation period in 2005 and 2006. Microarray analyses were conducted on leaves from trees grown in the field under ambient and twice-ambient ozone concentrations at Kranzberger Forst (Bavaria). Beech trees changed their transcript levels in response to ozone. In the years 2005 and 2006 different transcription patterns were observed; this may have been a result of different weather conditions and ozone uptake. Furthermore, we obtained differences in mRNA expression patterns between shade and sun leaves. In the ozone-treated sun leaves of 2005, slightly up- and down-regulated transcript levels were detected, particularly in the spring and autumn, whereas shade leaves clearly exhibited reduced mRNA levels, particularly at the end of the vegetation period. In 2006, this pattern could not be confirmed, and in the autumn, four other transcripts were slightly up-regulated in ozone-treated shade leaves. In addition, two other transcripts were found to be influenced in sun leaves in the spring/summer. While we detected changes in the levels of only a few transcripts, the observed effects were not identical in both years. In conclusion, elevated ozone exhibited very small influence on the transcription levels of genes of mature beech trees.

Ozone fumigation (twice ambient) reduces leaf infestation following natural and artificial inoculation by the endophytic fungus Apiognomonia errabunda of adult European beech trees

In 2006, a controlled infection study was performed in the 'Kranzberger Forst' to address the following questions: (1) Will massive artificial inoculation with Apiognomonia errabunda override the previously observed inhibitory effect of chronic ozone? (2) Can biochemical or molecular markers be detected to account for the action of ozone? To this end six adult beech trees were chosen, three ozone fumigated (2x ozone) and three control trees (ambient = 1x ozone). Spore-sprayed branches of sun and shade crown positions of each of the trees, and uninoculated control branches, were enclosed in 100-L plastic bags for one night to facilitate infection initiation. Samples were taken within a five-week period after inoculation. A. errabunda infestation levels quantified by real-time PCR increased in leaves that were not fumigated with additional ozone. Cell wall components and ACC (ethylene precursor 1-amino cyclopropane-1-carboxylic acid) increased upon ozone fumigation and may in part lead to the repression of fungal infection.

Mechanisms of ozone tolerance in rice: characterization of two QTLs affecting leaf bronzing by gene expression profiling and biochemical analyses

High surface ozone concentration is increasingly being recognized as a factor that negatively affects crop yields in Asia. However, little progress has been made in developing ozone-tolerant genotypes of rice-Asia's major staple crop. This study aimed to identify possible tolerance mechanisms by characterizing two quantitative trait loci (QTLs) that were previously shown to influence visible leaf symptoms under ozone exposure (120 nl l(-1), 7 h d(-1), 13 d). Two chromosome segment substitution lines (SL15 and SL41) that carried introgressions of the QTLs OzT3 and OzT9, respectively, were exposed to ozone at 120 nl l(-1) along with their parent Nipponbare. In accordance with the expected QTL effect, SL15 showed stronger visible symptoms of ozone damage than Nipponbare, whereas SL41 had fewer symptoms. Gene expression profiling by microarray hybridization yielded 470 probes that were differentially expressed in SL15 and 314 in SL41. Potential tolerance mechanisms were evaluated by investigating changes in gene expression in three general categories. (i) Processes involved in programmed cell death, in which a number of genes related to ethylene or jasmonic acid metabolism or general disease resistance were identified that were differentially regulated in one of the substitution lines. (ii) Biosynthesis of antioxidants. Testing this hypothesis did not reveal any genes differentially regulated between genotypes, and it was thus rejected. (iii) Turnover of antioxidants and enzymatic detoxification of radical oxygen species (ROS), in which a number of differentially regulated genes were also identified. Genes encoding antioxidant enzymes (catalase and peroxidases) tended to be more strongly expressed in SL15. A potential tolerance gene which encodes a putative ascorbate oxidase was identified within the QTL introgression in SL41. This gene showed consistently lower expression in SL41 under ozone exposure across different points in time within independent experiments. Its expression may be involved in mechanisms leading to enhanced ascorbic acid status in SL41 under ozone exposure, and may be linked to a higher concentration of total apoplastic ascorbic acid in SL41 that was observed in an independent experiment.

Gene expression profiling of ozone-treated Arabidopsis abi1td insertional mutant: protein phosphatase 2C ABI1 modulates biosynthesis ratio of ABA and ethylene

We report on the characterization of the interaction between reactive oxygen species signalling and abscisic acid (ABA)-mediated gene network in ozone (O(3)) stress response. To identify the stress-related signalling pathways and possible cross-talk controlled by an ABA-negative regulator, the protein phosphatase 2C abscisic acid insensitive1 (ABI1), we performed a genome-wide transcription profiling of O(3)-treated wild-type and ABI1 knockout (abi1td) plants. In addition, to better understand ABA signalling and the interactions between stress response pathways, we performed a microarray analysis of drought-treated plants. Functional categorization of the identified genes showed that ABI1 is involved in the modulation of several cellular processes including metabolism, transport, development, information pathways and variant splicing. Comparisons with available transcriptome data sets revealed the extent of ABI1 involvement in both ABA-dependent and ABA-independent gene expression. Furthermore, in O(3) stress the ABA hypersensitivity of abi1td resulted in a significant reduction of the ABA level, ethylene (ET) over-production and O(3) tolerance. Moreover, the physical interaction of ABI1 with ACC synthase2 and ACC synthase6 was shown. We provide a model explaining how ABI1 can regulate both ABA and ET biosynthesis. Altogether, our findings indicate that ABI1 plays the role of a general signal transducer linking ABA and ET biosynthesis as well as signalling pathways to O(3) stress tolerance.

Ethylene and salicylic acid control glutathione biosynthesis in ozone-exposed Arabidopsis thaliana

Ozone produces reactive oxygen species and induces the synthesis of phytohormones, including ethylene and salicylic acid. These phytohormones act as signal molecules that enhance cell death in response to ozone exposure. However, some studies have shown that ethylene and salicylic acid can instead decrease the magnitude of ozone-induced cell death. Therefore, we studied the defensive roles of ethylene and salicylic acid against ozone. Unlike the wild-type, Col-0, Arabidopsis mutants deficient in ethylene signaling (ein2) or salicylic acid biosynthesis (sid2) generated high levels of superoxide and exhibited visible leaf injury, indicating that ethylene and salicylic acid can reduce ozone damage. Macroarray analysis suggested that the ethylene and salicylic acid defects influenced glutathione (GSH) metabolism. Increases in the reduced form of GSH occurred in Col-0 6 h after ozone exposure, but little GSH was detected in ein2 and sid2 mutants, suggesting that GSH levels were affected by ethylene or salicylic acid signaling. We performed gene expression analysis by real-time polymerase chain reaction using genes involved in GSH metabolism. Induction of gamma-glutamylcysteine synthetase (GSH1), glutathione synthetase (GSH2), and glutathione reductase 1 (GR1) expression occurred normally in Col-0, but at much lower levels in ein2 and sid2. Enzymatic activities of GSH1 and GSH2 in ein2 and sid2 were significantly lower than in Col-0. Moreover, ozone-induced leaf damage observed in ein2 and sid2 was mitigated by artificial elevation of GSH content. Our results suggest that ethylene and salicylic acid protect against ozone-induced leaf injury by increasing de novo biosynthesis of GSH.

Learning from evolution: Thellungiella generates new knowledge on essential and critical components of abiotic stress tolerance in plants

Thellungiella salsuginea (halophila) is a close relative of Arabidopsis thaliana but, unlike A. thaliana, it grows well in extreme conditions of cold, salt, and drought as well as nitrogen limitation. Over the last decade, many laboratories have started to use Thellungiella to investigate the physiological, metabolic, and molecular mechanisms of abiotic stress tolerance in plants, and new knowledge has been gained in particular with respect to ion transport and gene expression. The advantage of Thellungiella over other extremophile model plants is that it can be directly compared with Arabidopsis, and therefore generate information on both essential and critical components of stress tolerance. Thellungiella research is supported by a growing body of technical resources comprising physiological and molecular protocols, ecotype collections, expressed sequence tags, cDNA-libraries, microarrays, and a pending genome sequence. This review summarizes the current state of knowledge on Thellungiella and re-evaluates its usefulness as a model for research into plant stress tolerance.

The challenge of making ozone risk assessment for forest trees more mechanistic

Upcoming decades will experience increasing atmospheric CO2 and likely enhanced O3 exposure which represents a risk for the carbon sink strength of forests, so that the need for cause-effect related O3 risk assessment increases. Although assessment will gain in reliability on an O3 uptake basis, risk is co-determined by the effective dose, i.e. the plant's sensitivity per O3 uptake. Recent progress in research on the molecular and metabolic control of the effective O3 dose is reported along with advances in empirically assessing O3 uptake at the whole-tree and stand level. Knowledge on both O3 uptake and effective dose (measures of stress avoidance and tolerance, respectively) needs to be understood mechanistically and linked as a pre-requisite before practical use of process-based O3 risk assessment can be implemented. To this end, perspectives are derived for validating and promoting new O3 flux-based modelling tools.

Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila

BACKGROUND

Thellungiella halophila (also known as Thellungiella salsuginea) is a model halophyte with a small plant size, short life cycle, and small genome. It easily undergoes genetic transformation by the floral dipping method used with its close relative, Arabidopsis thaliana. Thellungiella genes exhibit high sequence identity (approximately 90% at the cDNA level) with Arabidopsis genes. Furthermore, Thellungiella not only shows tolerance to extreme salinity stress, but also to chilling, freezing, and ozone stress, supporting the use of Thellungiella as a good genomic resource in studies of abiotic stress tolerance.

RESULTS

We constructed a full-length enriched Thellungiella (Shan Dong ecotype) cDNA library from various tissues and whole plants subjected to environmental stresses, including high salinity, chilling, freezing, and abscisic acid treatment. We randomly selected about 20,000 clones and sequenced them from both ends to obtain a total of 35 171 sequences. CAP3 software was used to assemble the sequences and cluster them into 9569 nonredundant cDNA groups. We named these cDNAs "RTFL" (RIKEN Thellungiella Full-Length) cDNAs. Information on functional domains and Gene Ontology (GO) terms for the RTFL cDNAs were obtained using InterPro. The 8289 genes assigned to InterPro IDs were classified according to the GO terms using Plant GO Slim. Categorical comparison between the whole Arabidopsis genome and Thellungiella genes showing low identity to Arabidopsis genes revealed that the population of Thellungiella transport genes is approximately 1.5 times the size of the corresponding Arabidopsis genes. This suggests that these genes regulate a unique ion transportation system in Thellungiella.

CONCLUSION

As the number of Thellungiella halophila (Thellungiella salsuginea) expressed sequence tags (ESTs) was 9388 in July 2008, the number of ESTs has increased to approximately four times the original value as a result of this effort. Our sequences will thus contribute to correct future annotation of the Thellungiella genome sequence. The full-length enriched cDNA clones will enable the construction of overexpressing mutant plants by introduction of the cDNAs driven by a constitutive promoter, the complementation of Thellungiella mutants, and the determination of promoter regions in the Thellungiella genome.

Molecular and physiological adaptation to prolonged drought stress in the leaves of two Andean potato genotypes

Responses to prolonged drought and recovery from drought of two South American potato (Solanum tuberosum L. ssp. andigena (Juz & Buk) Hawkes) landraces, Sullu and Ccompis were compared under field conditions. Physiological and biomass measurements, yield analysis, the results of hybridisation to a potato microarray platform (44 000 probes) and metabolite profiling were used to characterise responses to water deficit. Drought affected shoot and root biomass negatively in Ccompis but not in Sullu, whereas both genotypes maintained tuber yield under water stress. Ccompis showed stronger reduction in maximum quantum yield under stress than Sullu, and less decrease in stomatal resistance. Genes associated with PSII functions were activated during recovery in Sullu only. Evidence for sucrose accumulation in Sullu only during maximum stress and recovery was observed, in addition to increases in cell wall biosynthesis. A depression in the abundance of plastid superoxide dismutase transcripts was observed under maximum stress in Ccompis. Both sucrose and the regulatory molecule trehalose accumulated in the leaves of Sullu only. In contrast, in Ccompis, the raffinose oligosaccharide family pathway was activated, whereas low levels of sucrose and minor stress-mediated changes in trehalose were observed. Proline, and expression of the associated genes, rose in both genotypes under drought, with a 3-fold higher increase in Sullu than in Ccompis. The results demonstrate the presence of distinct molecular and biochemical drought responses in the two potato landraces leading to yield maintenance but differential biomass accumulation in vegetative tissues.

Gene networks in plant ozone stress response and tolerance

For many plant species ozone stress has become much more severe in the last decade. The accumulating evidence for the significant effects of ozone pollutant on crop and forest yield situate ozone as one of the most important environmental stress factors that limits plant productivity worldwide. Today, transcriptomic approaches seem to give the best coverage of genome level responses. Therefore, microarray serves as an invaluable tool for global gene expression analyses, unravelling new information about gene pathways, in-species and cross-species gene expression comparison, and for the characterization of unknown relationships between genes. In this review we summarize the recent progress in the transcriptomics of ozone to demonstrate the benefits that can be harvested from the application of integrative and systematic analytical approaches to study ozone stress response. We focused our consideration on microarray analyses identifying gene networks responsible for response and tolerance to elevated ozone concentration. From these analyses it is now possible to notice how plant ozone defense responses depend on the interplay between many complex signaling pathways and metabolite signals.

Elevated ozone alters soybean-virus interaction

Increasing concentrations of ozone (O(3)) in the troposphere affect many organisms and their interactions with each other. To analyze the changes in a plant-pathogen interaction, soybean plants were infected with Soybean mosaic virus (SMV) while they were fumigated with O(3). In otherwise natural field conditions, elevated O(3) treatment slowed systemic infection and disease development by inducing a nonspecific resistance against SMV for a period of 3 weeks. During this period, the negative effect of virus infection on light-saturated carbon assimilation rate was prevented by elevated O(3) exposure. To identify the molecular basis of a soybean nonspecific defense response, high-throughput gene expression analysis was performed in a controlled environment. Transcripts of fungal, bacterial, and viral defense-related genes, including PR-1, PR-5, PR-10, and EDS1, as well as genes of the flavonoid biosynthesis pathways (and concentrations of their end products, quercetin and kaempherol derivatives) increased in response to elevated O(3). The drastic changes in soybean basal defense response under altered atmospheric conditions suggest that one of the elements of global change may alter the ecological consequences and, eventually, coevolutionary relationship of plant-pathogen interactions in the future.

Modification of the biochemical pathways of plants induced by ozone: what are the varied routes to change?

When plants are observed under a low dose of ozone, some physiological and metabolic shifts occur. Barring extreme injury such as tissue damage or stomata closure, most of these disruptive changes are likely to have been initiated at the level of gene expression. The belief is oxidative products formed in ozone exposed leaves, e.g. hydrogen peroxide, are responsible for much of the biochemical adjustments. The first line of defense is a range of antioxidants, such as ascorbate and glutathione, but if this defense is overwhelmed, subsequent actions occur, similar to systemic acquired resistance or general wounding. Yet there are seemingly unrelated metabolic responses which are also triggered, such as early senescence. We discuss here the current understanding of gene control and signal transduction/control in order to increase our comprehension of how ozone alters the basic metabolism of plants and how plants counteract or cope with ozone.

The Arabidopsis thaliana carboxyl-terminal domain phosphatase-like 2 regulates plant growth, stress and auxin responses

More than 20 genes in the Arabidopsis genome encode proteins similar to phosphatases that act on the carboxyl-terminal domain (CTD) of RNA polymerase II. One of these CTD-phosphatase-like (CPL) proteins, CPL2, dephosphorylates CTD-Ser5-PO4 in an intact RNA polymerase II complex and contains a double-stranded (ds)-RNA-binding motif (DRM). Although the dsRNA-binding activity of CPL2 DRM has not been shown to date, T-DNA insertion mutants that express CPL2 variants lacking either a part of DRM (cpl2-1) or the entire DRM (cpl2-2) exhibited leaf expansion defects, early flowering, low fertility, and increased salt sensitivity. cpl2 mutant plants produced shorter hypocotyls than wild-type plants in the light, but were indistinguishable from wild type in the dark. CPL2 was expressed in shoot and root meristems and vasculatures, expanding rosette leaves, and floral organs suggesting a focal role for growth. Microarray and RT-PCR analyses revealed that basal levels of several auxin-responsive transcripts were reduced in cpl2. On the other hand, the levels of endogenous auxin and its conjugates were similar in wild type and cpl2. Overexpression of ARF5 but not all activator ARF transcription factors restored the auxin-responsive DR5-GUS reporter gene expression and the leaf expansion of cpl2 mutant plants but not early flowering phenotype. These results establish CPL2 as a multifunctional regulator that modulates plant growth, stress, and auxin responses.

The E subunit of photosystem I is not essential for linear electron flow and photoautotrophic growth in Arabidopsis thaliana

PSI-E is part of the stromal side of photosystem I (PSI). In Arabidopsis thaliana, the two nuclear genes PsaE1 and PsaE2 code for PSI-E, and transcripts of PsaE1 are markedly more abundant than PsaE2 transcripts. Stable null alleles of the two PsaE genes, psae1-3 and psae2-1, were identified and characterised. The psae2-1 mutant exhibited wild-type like PSI-E abundance and photosynthetic performance, whereas in the psae1-3 mutant PSI-E accumulation was decreased by 85%, together with an impaired thylakoid electron flow and plant growth rate. The psae1-3 psae2-1 double mutant totally lacked PSI-E but was still able to grow photoautotrophically, implying that PSI-E is not essential for PSI accumulation and thylakoid electron flow.

Early PLDalpha-mediated events in response to progressive drought stress in Arabidopsis: a transcriptome analysis

Phospholipase D (PLD) has been implicated in a variety of stresses including osmotic stress and wounding. PLDalpha1-derived phosphatidic acid interacts with ABI1 phosphatase 2C and promotes abscisic acid signalling. It has also been shown to regulate proline biosynthesis negatively. Plants with abrogated PLDalpha show insensitivity to abscisic acid (ABA) and impaired stomatal conductance. The goal in the present study was to identify early PLDalpha-mediated events in response to progressive drought stress in Arabidopsis. Water was withheld from 7-week-old Arabidopsis thaliana (Col-0) and antisense-PLDalpha1 (anti-PLDalpha) in a controlled environment chamber. Diurnal leaf water potential (LWP) and photosynthesis measurements were recorded five and three times a day, respectively. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and microarray analyses were conducted using RNA from shoots collected at the fourth LWP time point on the ninth day after stress imposition. Anti-PLDalpha experienced severe water stress (-1.28 MPa) at the same time period that Col-0 experienced less water stress (-0.31 MPa). Diurnal LWP measurements showed that anti-PLDalpha had a lower LWP than Col-0 in both control and drought-stress conditions. Photosynthesis was also more affected in anti-PLDalpha than in Col-0. Anti-PLDalpha plants recovered fully following rehydration after 10 d of stress. qRT-PCR revealed up to 18-fold lower values for PLDalpha transcripts in stressed anti-PLDalpha plants when compared with stressed Col-0. Microarray expression profiles revealed distinct gene expression patterns in Col-0 and anti-PLDalpha. No differences in gene expression were detected between the two genotypes in the absence of drought stress. ROP8, PLDdelta, and lipid transfer proteins were among the differentially expressed genes between the two genotypes.

DNA Microarray Analyses in Higher Plants

DNA microarrays were originally devised and described as a convenient technology for the global analysis of plant gene expression. Over the past decade, their use has expanded enormously to cover all kingdoms of living organisms. At the same time, the scope of applications of microarrays has increased beyond expression analyses, with plant genomics playing a leadership role in the on-going development of this technology. As the field has matured, the rate-limiting step has moved from that of the technical process of data generation to that of data analysis. We currently face major problems in dealing with the accumulating datasets, not simply with respect to how to archive, access, and process the huge amounts of data that have been and are being produced, but also in determining the relative quality of the different datasets. A major recognized concern is the appropriate use of statistical design in microarray experiments, without which the datasets are rendered useless. A vigorous area of current research involves the development of novel statistical tools specifically for microarray experiments. This article describes, in a necessarily selective manner, the types of platforms currently employed in microarray research and provides an overview of recent activities using these platforms in plant biology.

Response diversity of Arabidopsis thaliana ecotypes in elevated [CO2] in the field

Free Air [CO(2)] Enrichment (FACE) allows for plant growth under fully open-air conditions of elevated [CO(2)] at concentrations expected to be reached by mid-century. We used Arabidopsis thaliana ecotypes Col-0, Cvi-0, and WS to analyze changes in gene expression and metabolite profiles of plants grown in "SoyFACE" (http://www.soyface.uiuc.edu/), a system of open-air rings within which [CO(2)] is elevated to approximately 550 ppm. Data from multiple rings, comparing plants in ambient air and elevated [CO(2)], were analyzed by mixed model ANOVA, linear discriminant analysis (LDA) and data-mining tools. In elevated [CO(2)], decreases in the expression of genes related to chloroplast functions characterized all lines but individual members of distinct multi-gene families were regulated differently between lines. Also, different strategies distinguished the lines with respect to the regulation of genes related to carbohydrate biosynthesis and partitioning, N-allocation and amino acid metabolism, cell wall biosynthesis, and hormone responses, irrespective of the plants' developmental status. Metabolite results paralleled reactions seen at the level of transcript expression. Evolutionary adaptation of species to their habitat and intrinsic genetic plasticity seem to determine the nature of responses to elevated [CO(2)]. Irrespective of their underlying genetic diversity, and evolutionary adaptation to different habitats, a small number of common, predominantly stress-responsive, signature transcripts appear to characterize responses of the Arabidopsis ecotypes in FACE.