TY - JOUR AB - Pectin- and hemicellulose-associated structures of plant cell walls participate in defense responses against pathogens of different parasitic lifestyles. The resulting immune responses incorporate phytohormone signaling components associated with salicylic acid (SA) and jasmonic acid (JA). SA plays a pivotal role in systemic acquired resistance (SAR), a form of induced resistance that - after a local immune stimulus - confers long-lasting, systemic protection against a broad range of biotrophic invaders. β-D-XYLOSIDASE 4 (BXL4) protein accumulation is enhanced in the apoplast of plants undergoing SAR. Here, two independent Arabidopsis thaliana mutants of BXL4 displayed compromised systemic defenses, while local resistance responses to Pseudomonas syringae remained largely intact. Because both phloem-mediated and airborne systemic signaling were abrogated in the mutants, the data suggest that BXL4 is a central component in SAR signaling mechanisms. Exogenous xylose, a possible product of BXL4 enzymatic activity in plant cell walls, enhanced systemic defenses. However, GC-MS analysis of SAR-activated plants revealed BXL4-associated changes in the accumulation of certain amino acids and soluble sugars, but not xylose. In contrast, the data suggest a possible role of pectin-associated fucose as well as of the polyamine putrescine as regulatory components of SAR. This is the first evidence of a central role of cell wall metabolic changes in systemic immunity. Additionally, the data reveal a so far unrecognized complexity in the regulation of SAR, which might allow the design of (crop) plant protection measures including SAR-associated cell wall components. AU - Bauer, K. AU - Nayem, S. AU - Lehmann, M.* AU - Wenig, M. AU - Shu, L.J.* AU - Ranf, S.* AU - Geigenberger, P.* AU - Vlot, A.C. C1 - 67544 C2 - 55009 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - β-D-XYLOSIDASE 4 modulates systemic immune signaling in Arabidopsis thaliana. JO - Front. Plant Sci. VL - 13 PB - Frontiers Media Sa PY - 2023 SN - 1664-462X ER - TY - JOUR AB - The beneficial effect of microbial consortium application on plants is strongly affected by soil conditions, which are influenced by farming practices. The establishment of microbial inoculants in the rhizosphere is a prerequisite for successful plant-microorganism interactions. This study investigated whether a consortium of beneficial microorganisms establishes in the rhizosphere of a winter crop during the vegetation period, including the winter growing season. In addition, we aimed for a better understanding of its effect on plant performance under different farming practices. Winter rye plants grown in a long-time field trial under conventional or organic farming practices were inoculated after plant emergence in autumn with a microbial consortium containing Pseudomonas sp. (RU47), Bacillus atrophaeus (ABi03) and Trichoderma harzianum (OMG16). The density of the microbial inoculants in the rhizosphere and root-associated soil was quantified in autumn and the following spring. Furthermore, the influence of the consortium on plant performance and on the rhizosphere bacterial community assembly was investigated using a multidisciplinary approach. Selective plating showed a high colonization density of individual microorganisms of the consortium in the rhizosphere and root-associated soil of winter rye throughout its early growth cycle. 16S rRNA gene amplicon sequencing showed that the farming practice affected mainly the rhizosphere bacterial communities in autumn and spring. However, the microbial consortium inoculated altered also the bacterial community composition at each sampling time point, especially at the beginning of the new growing season in spring. Inoculation of winter rye with the microbial consortium significantly improved the plant nutrient status and performance especially under organic farming. In summary, the microbial consortium showed sufficient efficacy throughout vegetation dormancy when inoculated in autumn and contributed to better plant performance, indicating the potential of microbe-based solutions in organic farming where nutrient availability is limited. AU - Behr, J.H.* AU - Kampouris, I.D.* AU - Babin, D.* AU - Sommermann, L.* AU - Francioli, D.* AU - Kuhl-Nagel, T.* AU - Chowdhury, S.P. AU - Geistlinger, J.* AU - Smalla, K.* AU - Neumann, G.* AU - Grosch, R.* C1 - 68288 C2 - 54797 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Beneficial microbial consortium improves winter rye performance by modulating bacterial communities in the rhizosphere and enhancing plant nutrient acquisition. JO - Front. Plant Sci. VL - 14 PB - Frontiers Media Sa PY - 2023 SN - 1664-462X ER - TY - JOUR AB - Seed dormancy is a crucial developmental transition that affects the adaption and survival of plants. Arabidopsis DELAY OF GERMINATION 1 (DOG1) is known as a master regulator of seed dormancy. However, although several upstream factors of DOG1 have been reported, the exact regulation of DOG1 is not fully understood. Histone acetylation is an important regulatory layer, controlled by histone acetyltransferases and histone deacetylases. Histone acetylation strongly correlates with transcriptionally active chromatin, whereas heterochromatin is generally characterized by hypoacetylated histones. Here we describe that loss of function of two plant-specific histone deacetylases, HD2A and HD2B, resulted in enhanced seed dormancy in Arabidopsis. Interestingly, the silencing of HD2A and HD2B caused hyperacetylation of the DOG1 locus and promoted the expression of DOG1 during seed maturation and imbibition. Knockout of DOG1 could rescue the seed dormancy and partly rescue the disturbed development phenotype of hd2ahd2b. Transcriptomic analysis of the hd2ahd2b line shows that many genes involved in seed development were impaired. Moreover, we demonstrated that HSI2 and HSL1 interact with HD2A and HD2B. In sum, these results suggest that HSI2 and HSL1 might recruit HD2A and HD2B to DOG1 to negatively regulate DOG1 expression and to reduce seed dormancy, consequently, affecting seed development during seed maturation and promoting seed germination during imbibition. AU - Han, Y. AU - Georgii, E. AU - Priego-Cubero, S.* AU - Wurm, C. AU - Hüther, P.* AU - Huber, G.* AU - Koller, R.* AU - Becker, C.* AU - Durner, J. AU - Lindermayr, C. C1 - 68525 C2 - 54697 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Arabidopsis histone deacetylase HD2A and HD2B regulate seed dormancy by repressing DELAY OF GERMINATION 1. JO - Front. Plant Sci. VL - 14 PB - Frontiers Media Sa PY - 2023 SN - 1664-462X ER - TY - JOUR AB - Plants are central to complex networks of multitrophic interactions. Increasing evidence suggests that beneficial microorganisms (BMs) may be used as plant biostimulants and pest biocontrol agents. We investigated whether tomato (Solanum lycopersicum) plants are thoroughly colonized by the endophytic and entomopathogenic fungus Beauveria bassiana, and how such colonization affects physiological parameters and the phenotype of plants grown under unstressed conditions or exposed to the pathogenic fungus Botrytis cinerea. As a positive control, a strain of the well-known biocontrol agent and growth inducer Trichoderma afroharzianum was used. As multitrophic interactions are often driven by (or have consequences on) volatile organic compounds (VOCs) released by plants constitutively or after induction by abiotic or biotic stresses, VOC emissions were also studied. Both B. bassiana and T. afroharzianum induced a significant but transient (one to two-day-long) reduction of stomatal conductance, which may indicate rapid activation of defensive (rejection) responses, but also limited photosynthesis. At later stages, our results demonstrated a successful and complete plant colonization by B. bassiana, which induced higher photosynthesis and lower respiration rates, improved growth of roots, stems, leaves, earlier flowering, higher number of fruits and yield in tomato plants. Beauveria bassiana also helped tomato plants fight B. cinerea, whose symptoms in leaves were almost entirely relieved with respect to control plants. Less VOCs were emitted when plants were colonized by B. bassiana or infected by B. cinerea, alone or in combination, suggesting no activation of VOC-dependent defensive mechanisms in response to both fungi. AU - Russo, A.* AU - Winkler, J.B. AU - Ghirardo, A. AU - Monti, M.M.* AU - Pollastri, S.* AU - Ruocco, M.* AU - Schnitzler, J.-P. AU - Loreto, F.* C1 - 69001 C2 - 53802 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Interaction with the entomopathogenic fungus Beauveria bassiana influences tomato phenome and promotes resistance to Botrytis cinerea infection. JO - Front. Plant Sci. VL - 14 PB - Frontiers Media Sa PY - 2023 SN - 1664-462X ER - TY - JOUR AB - In the past, most grapevine trunk diseases (GTDs) have been controlled by treatments with sodium arsenite. For obvious reasons, sodium arsenite was banned in vineyards, and consequently, the management of GTDs is difficult due to the lack of methods with similar effectiveness. Sodium arsenite is known to have a fungicide effect and to affect the leaf physiology, but its effect on the woody tissues where the GTD pathogens are present is still poorly understood. This study thus focuses on the effect of sodium arsenite in woody tissues, particularly in the interaction area between asymptomatic wood and necrotic wood resulting from the GTD pathogens' activities. Metabolomics was used to obtain a metabolite fingerprint of sodium arsenite treatment and microscopy to visualize its effects at the histo-cytological level. The main results are that sodium arsenite impacts both metabolome and structural barriers in plant wood. We reported a stimulator effect on plant secondary metabolites in the wood, which add to its fungicide effect. Moreover, the pattern of some phytotoxins is affected, suggesting the possible effect of sodium arsenite in the pathogen metabolism and/or plant detoxification process. This study brings new elements to understanding the mode of action of sodium arsenite, which is useful in developing sustainable and eco-friendly strategies to better manage GTDs. AU - Trouvelot, S.* AU - Lemaître-Guillier, C.* AU - Vallet, J.* AU - Jacquens, L.* AU - Douillet, A.* AU - Harir, M. AU - Larignon, P.* AU - Roullier-Gall, C.* AU - Schmitt-Kopplin, P.* AU - Adrian, M.* AU - Fontaine, F.* C1 - 67802 C2 - 54280 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Sodium arsenite-induced changes in the wood of esca-diseased grapevine at cytological and metabolomic levels. JO - Front. Plant Sci. VL - 14 PB - Frontiers Media Sa PY - 2023 SN - 1664-462X ER - TY - JOUR AB - Plants have evolved sophisticated mechanisms to cope with drought, which involve massive changes in nuclear gene expression. However, little is known about the roles of post-transcriptional processing of nuclear or organellar transcripts and how meaningful these changes are. To address these issues, we used RNA-sequencing after ribosomal RNA depletion to monitor (post)transcriptional changes during different times of drought exposure in Arabidopsis Col-0. Concerning the changes detected in the organellar transcriptomes, chloroplast transcript levels were globally reduced, editing efficiency dropped, but splicing was not affected. Mitochondrial transcripts were slightly elevated, while editing and splicing were unchanged. Conversely, alternative splicing (AS) affected nearly 1,500 genes (9% of expressed nuclear genes). Of these, 42% were regulated solely at the level of AS, representing transcripts that would have gone unnoticed in a microarray-based approach. Moreover, we identified 927 isoform switching events. We provide a table of the most interesting candidates, and as proof of principle, increased drought tolerance of the carbonic anhydrase ca1 and ca2 mutants is shown. In addition, altering the relative contributions of the spliced isoforms could increase drought resistance. For example, our data suggest that the accumulation of a nonfunctional FLM (FLOWERING LOCUS M) isoform and not the ratio of FLM-ß and -δ isoforms may be responsible for the phenotype of early flowering under long-day drought conditions. In sum, our data show that AS enhances proteome diversity to counteract drought stress and represent a valuable resource that will facilitate the development of new strategies to improve plant performance under drought. AU - Xu, D.* AU - Tang, Q.* AU - Xu, P. AU - Schäffner, A. AU - Leister, D.* AU - Kleine, T.* C1 - 68041 C2 - 54519 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Response of the organellar and nuclear (post)transcriptomes of Arabidopsis to drought. JO - Front. Plant Sci. VL - 14 PB - Frontiers Media Sa PY - 2023 SN - 1664-462X ER - TY - JOUR AU - Correa-Aragunde, N.* AU - Foresi, N.* AU - Lindermayr, C. AU - Petřivalský, M.* C1 - 64789 C2 - 52485 TI - Editorial: Functions of nitric oxide in photosynthetic organisms. JO - Front. Plant Sci. VL - 13 PY - 2022 SN - 1664-462X ER - TY - JOUR AB - High doses of ozone (O3) and nitrogen dioxide (NO2) cause damage and cell death in plants. These two gases are among the most harmful air pollutants for ecosystems and therefore it is important to understand how plant resistance or sensitivity to these gases work at the molecular level and its genetic control. We compared transcriptome data from O3 and NO2 fumigations to other cell death related treatments, as well as individual marker gene transcript level in different Arabidopsis thaliana accessions. Our analysis revealed that O3 and NO2 trigger very similar gene expression responses that include genes involved in pathogen resistance, cell death and ethylene signaling. However, we also identified exceptions, for example RBOHF encoding a reactive oxygen species producing RESPIRATORY BURST OXIDASE PROTEIN F. This gene had increased transcript levels by O3 but decreased transcript levels by NO2, showing that plants can identify each of the gases separately and activate distinct signaling pathways. To understand the genetics, we conducted a genome wide association study (GWAS) on O3 and NO2 tolerance of natural Arabidopsis accessions. Sensitivity to both gases seem to be controlled by several independent small effect loci and we did not find an overlap in the significantly associated regions. Further characterization of the GWAS candidate loci identified new regulators of O3 and NO2 induced cell death including ABH1, a protein that functions in abscisic acid signaling, mRNA splicing and miRNA processing. The GWAS results will facilitate further characterization of the control of programmed cell death and differences between oxidative and nitrosative stress in plants. AU - Leppälä, J.* AU - Gaupels, F. AU - Xu, E.* AU - Morales, L.O.* AU - Durner, J. AU - Brosché, M.* C1 - 66600 C2 - 53224 TI - Ozone and nitrogen dioxide regulate similar gene expression responses in Arabidopsis but natural variation in the extent of cell death is likely controlled by different genetic loci. JO - Front. Plant Sci. VL - 13 PY - 2022 SN - 1664-462X ER - TY - JOUR AU - Hartmann, A.* AU - Klink, S. AU - Rothballer, M. C1 - 62300 C2 - 50761 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Plant growth promotion and induction of systemic tolerance to drought and salt stress of plants by quorum sensing auto-inducers of the N-acyl-homoserine lactone type: Recent developments. JO - Front. Plant Sci. VL - 12 PB - Frontiers Media Sa PY - 2021 SN - 1664-462X ER - TY - JOUR AB - Clubroot, caused by Plasmodiophora brassicae infection, is a disease of growing importance in cruciferous crops, including oilseed rape (Brassica napus). The affected plants exhibit prominent galling of the roots that impairs their capacity for water and nutrient uptake, which leads to growth retardation, wilting, premature ripening, or death. Due to the scarcity of effective means of protection against the pathogen, breeding of resistant varieties remains a crucial component of disease control measures. The key aspect of the breeding process is the identification of genetic factors associated with variable response to the pathogen exposure. Although numerous clubroot resistance loci have been described in Brassica crops, continuous updates on the sources of resistance are necessary. Many of the resistance genes are pathotype-specific, moreover, resistance breakdowns have been reported. In this study, we characterize the clubroot resistance locus in the winter oilseed rape cultivar "Tosca." In a series of greenhouse experiments, we evaluate the disease severity of P. brassicae-challenged "Tosca"-derived population of doubled haploids, which we genotype with Brassica 60 K array and a selection of SSR/SCAR markers. We then construct a genetic map and narrow down the resistance locus to the 0.4 cM fragment on the A03 chromosome, corresponding to the region previously described as Crr3. Using Oxford Nanopore long-read genome resequencing and RNA-seq we review the composition of the locus and describe a duplication of TIR-NBS-LRR gene. Further, we explore the transcriptomic differences of the local genes between the clubroot resistant and susceptible, inoculated and control DH lines. We conclude that the duplicated TNL gene is a promising candidate for the resistance factor. This study provides valuable resources for clubroot resistance breeding programs and lays a foundation for further functional studies on clubroot resistance. AU - Kopec, P.M.* AU - Mikolajczyk, K.* AU - Jajor, E.* AU - Perek, A.* AU - Nowakowska, J.* AU - Obermeier, C.* AU - Chawla, H.S. AU - Korbas, M.* AU - Bartkowiak-Broda, I.* AU - Karlowski, W.M.* C1 - 61956 C2 - 50534 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Local duplication of TIR-NBS-LRR gene marks clubroot resistance in Brassica napus cv. Tosca. JO - Front. Plant Sci. VL - 12 PB - Frontiers Media Sa PY - 2021 SN - 1664-462X ER - TY - JOUR AU - Lindermayr, C. AU - Oracz, K.* AU - Cuypers, A.* AU - Schnitzler, J.-P. AU - Durner, J. C1 - 61381 C2 - 49831 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Editorial: Highlights of POG 2019 - Plant Oxygen Group Conference. JO - Front. Plant Sci. VL - 12 PB - Frontiers Media Sa PY - 2021 SN - 1664-462X ER - TY - JOUR AB - Photosynthesis is the major process leading to primary production in the Biosphere. There is a total of 7000bn tons of CO(2)in the atmosphere and photosynthesis fixes more than 100bn tons annually. The CO(2)assimilated by the photosynthetic apparatus is the basis of crop production and, therefore, of animal and human food. This has led to a renewed interest in photosynthesis as a target to increase plant production and there is now increasing evidence showing that the strategy of improving photosynthetic traits can increase plant yield. However, photosynthesis and the photosynthetic apparatus are both conditioned by environmental variables such as water availability, temperature, [CO2], salinity, and ozone. The "omics" revolution has allowed a better understanding of the genetic mechanisms regulating stress responses including the identification of genes and proteins involved in the regulation, acclimation, and adaptation of processes that impact photosynthesis. The development of novel non-destructive high-throughput phenotyping techniques has been important to monitor crop photosynthetic responses to changing environmental conditions. This wealth of data is being incorporated into new modeling algorithms to predict plant growth and development under specific environmental constraints. This review gives a multi-perspective description of the impact of changing environmental conditions on photosynthetic performance and consequently plant growth by briefly highlighting how major technological advances including omics, high-throughput photosynthetic measurements, metabolic engineering, and whole plant photosynthetic modeling have helped to improve our understanding of how the photosynthetic machinery can be modified by different abiotic stresses and thus impact crop production. AU - Baslam, M.* AU - Mitsui, T.* AU - Hodges, M.* AU - Priesack, E. AU - Herritt, M.T.* AU - Aranjuelo, I.* AU - Sanz-Sáez, Á.* C1 - 59794 C2 - 49043 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Photosynthesis in a changing global climate: Scaling up and scaling down in crops. JO - Front. Plant Sci. VL - 11 PB - Frontiers Media Sa PY - 2020 SN - 1664-462X ER - TY - JOUR AB - FIGURE LEGEND In the original article, there was a mistake in the legend for Figure 6 and Figure 7 as published. The numbering for Figure 6 was mixed with Figure 7 and not in agreement with the text: this mistake was introduced during proof stage, since the editing changed both legend and figure number. In addition, DC3000 should not be in italics. The correct numbering of Figures 6 and 7 appear below. FIGURE 6 | BCAA levels after exogenous application of 2-HAs to A. thaliana plants FIGURE 7 | ILA and LA abundance in response to P. syringae virulent strain infection. ERROR IN FIGURE In the original article, there was a mistake in Figures 2–4, and 6 as published. Due to the incorrect calculation of 2-HA level (a factor 50 was missed), all figures showing such measurements have to be replaced with the corrected y axis and limit of detection. The corrected Figures 2–4, and 7 appear below. (Figure presented.). AU - Maksym, R.P. AU - Ghirardo, A. AU - Zhang, W. AU - von Saint Paul, V. AU - Lange, B. AU - Geist, B. AU - Hajirezaei, M.R.* AU - Schnitzler, J.-P. AU - Schäffner, A. C1 - 59991 C2 - 49807 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - The defense-related isoleucic acid differentially accumulates in Arabidopsis among branched-chain amino acid-related 2-hydroxy carboxylic acids. (vol 9, 766, 2018). JO - Front. Plant Sci. VL - 11 PB - Frontiers Media Sa PY - 2020 SN - 1664-462X ER - TY - JOUR AB - Three-dimensional models of root growth, architecture and function are becoming important tools that aid the design of agricultural management schemes and the selection of beneficial root traits. However, while benchmarking is common in many disciplines that use numerical models, such as natural and engineering sciences, functional-structural root architecture models have never been systematically compared. The following reasons might induce disagreement between the simulation results of different models: different representation of root growth, sink term of root water and solute uptake and representation of the rhizosphere. Presently, the extent of discrepancies is unknown, and a framework for quantitatively comparing functional-structural root architecture models is required. We propose, in a first step, to define benchmarking scenarios that test individual components of complex models: root architecture, water flow in soil and water flow in roots. While the latter two will focus mainly on comparing numerical aspects, the root architectural models have to be compared at a conceptual level as they generally differ in process representation. Therefore, defining common inputs that allow recreating reference root systems in all models will be a key challenge. In a second step, benchmarking scenarios for the coupled problems are defined. We expect that the results of step 1 will enable us to better interpret differences found in step 2. This benchmarking will result in a better understanding of the different models and contribute toward improving them. Improved models will allow us to simulate various scenarios with greater confidence and avoid bugs, numerical errors or conceptual misunderstandings. This work will set a standard for future model development. AU - Schnepf, A.* AU - Black, C.K.* AU - Couvreur, V.* AU - Delory, B.M.* AU - Doussan, C.* AU - Koch, A.* AU - Koch, T.* AU - Javaux, M.* AU - Landl, M.* AU - Leitner, D.* AU - Lobet, G.* AU - Mai, T.H.* AU - Meunier, F.* AU - Petrich, L.* AU - Postma, J.A.* AU - Priesack, E. AU - Schmidt, V.* AU - Vanderborght, J.* AU - Vereecken, H.* AU - Weber, M.* C1 - 58896 C2 - 48503 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Call for participation: Collaborative benchmarking of functional-structural root architecture models. The case of root water uptake. JO - Front. Plant Sci. VL - 11 PB - Frontiers Media Sa PY - 2020 SN - 1664-462X ER - TY - JOUR AB - Nitrogen oxides (NOx), mainly a mixture of nitric oxide (NO) and nitrogen dioxide (NO2), are formed by the reaction of nitrogen and oxygen compounds in the air as a result of combustion processes and traffic. Both deposit into leaves via stomata, which on the one hand benefits air quality and on the other hand provides an additional source of nitrogen for plants. In this study, we first determined the NO and NO(2)specific deposition velocities based on projected leaf area (sV(d)) using a branch enclosure system. We studied four tree species that are regarded as suitable to be planted under predicted future urban climate conditions:Carpinus betulus,Fraxinus ornus,Fraxinus pennsylvanicaandOstrya carpinifolia. The NO and NO(2)sV(d)were found similar in all tree species. Second, in order to confirm NO metabolization, we fumigated plants with(15)NO and quantified the incorporation of(15)N in leaf materials of these trees and four additional urban tree species (Celtis australis,Alnus spaethii,Alnus glutinosa, andTilia henryana) under controlled environmental conditions. Based on these(15)N-labeling experiments,A. glutinosashowed the most effective incorporation of(15)NO. Third, we tried to elucidate the mechanism of metabolization. Therefore, we generated transgenic poplars overexpressingArabidopsis thalianaphytoglobin 1 or 2. Phytoglobins are known to metabolize NO to nitrate in the presence of oxygen. The(15)N uptake in phytoglobin-overexpressing poplars was significantly increased compared to wild-type trees, demonstrating that the NO uptake is enzymatically controlled besides stomatal dependence. In order to upscale the results and to investigate if a trade-off exists between air pollution removal and survival probability under future climate conditions, we have additionally carried out a modeling exercise of NO and NO(2)deposition for the area of central Berlin. If the actually dominant deciduous tree species (Acer platanoides,Tilia cordata,Fagus sylvatica,Quercus robur) would be replaced by the species suggested for future conditions, the total annual NO and NO(2)deposition in the modeled urban area would hardly change, indicating that the service of air pollution removal would not be degraded. These results may help selecting urban tree species in future greening programs. AU - Zhang, J. AU - Ghirardo, A. AU - Gori, A.* AU - Albert, A. AU - Buegger, F. AU - Pace, R.* AU - Georgii, E. AU - Grote, R.* AU - Schnitzler, J.-P. AU - Durner, J. AU - Lindermayr, C. C1 - 60324 C2 - 49207 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Improving air quality by nitric oxide consumption of climate-resilient trees suitable for urban greening. JO - Front. Plant Sci. VL - 11 PB - Frontiers Media Sa PY - 2020 SN - 1664-462X ER - TY - JOUR AB - Climate change is altering the dynamics of crop pests and diseases resulting in reduced crop yields. Using beneficial soil bacterial to increase crop health is a quickly developing area in sustainable agriculture, but it is unknown if climate change or interactions with other species could alter their effect. The plant growth-promoting rhizobacteriumAcidovorax radicisN35 is known to increase barley (Hordeum vulgare) plant growth under laboratory conditions, and we tested the stability of the plant-bacterial interactions when exposed to elevated carbon dioxide (CO2) and ozone (O-3) levels while infesting the aboveground leaves with cereal aphids (Sitobion avenae) and the soil with beneficial earthworms.Acidovorax radicisN35 increased plant growth and reduced insect growth - with greatest effect in a high-stress elevated O(3)environment, but reduced effects under elevated CO2. Earthworms promoted both plant and insect growth, but inoculation withA. radicisN35 alleviated some of the earthworm-mediated increase in pest abundance, particularly in the ambient environment. The consistency of these beneficial effects highlights the potential of exploiting local species interactions for predicting and mitigating climate change effects in managed systems. We conclude that microbial bioprotectants have high potential for benefiting agricultureviaplant-growth promotion and pest suppression. AU - Zytynska, S.E.* AU - Eicher, M.* AU - Rothballer, M. AU - Weisser, W.W.* C1 - 60168 C2 - 49285 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Microbial-mediated plant growth promotion and pest suppression varies under climate change. JO - Front. Plant Sci. VL - 11 PB - Frontiers Media Sa PY - 2020 SN - 1664-462X ER - TY - JOUR AB - Nitric oxide (NO) is a key signaling molecule in all kingdoms. In plants, NO is involved in the regulation of various processes of growth and development as well as biotic and abiotic stress response. It mainly acts by modifying protein cysteine or tyrosine residues or by interacting with protein bound transition metals. Thereby, the modification of cysteine residues known as protein S-nitrosation is the predominant mechanism for transduction of NO bioactivity. Histone acetylation on N-terminal lysine residues is a very important epigenetic regulatory mechanism. The transfer of acetyl groups from acetyl-coenzyme A on histone lysine residues is catalyzed by histone acetyltransferases. This modification neutralizes the positive charge of the lysine residue and results in a loose structure of the chromatin accessible for the transcriptional machinery. Histone deacetylases, in contrast, remove the acetyl group of histone tails resulting in condensed chromatin with reduced gene expression activity. In plants, the histone acetylation level is regulated by S-nitrosation. NO inhibits HDA complexes resulting in enhanced histone acetylation and promoting a supportive chromatin state for expression of genes. Moreover, methylation of histone tails and DNA are important epigenetic modifications, too. Interestingly, methyltransferases and demethylases are described as targets for redox molecules in several biological systems suggesting that these types of chromatin modifications are also regulated by NO. In this review article, we will focus on redox-regulation of histone acetylation/methylation and DNA methylation in plants, discuss the consequences on the structural level and give an overview where NO can act to modulate chromatin structure. AU - Ageeva-Kieferle, A. AU - Rudolf, E.E. AU - Lindermayr, C. C1 - 56299 C2 - 46981 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Redox-dependent chromatin remodeling: A new function of nitric oxide as architect of chromatin structure in plants. JO - Front. Plant Sci. VL - 10 PB - Frontiers Media Sa PY - 2019 SN - 1664-462X ER - TY - JOUR AB - Just imagine a Plant Science professor in front of a classroom full of interested and attentive students. Imagine what their answers to this intriguing question would be: “What are, according to you, the functions ensured by the plant cell nucleus?” It would be very surprising if some of them would answer cell signaling in response to biotic and abiotic stresses or developmental processes. Most of them would probably answer according to a classical point of view: DNA replication or gene expression. Hence it is still admitted in recent publications (see for instance Fedorenko et al., 2010) that molecules smaller than 40 kDa can diffuse freely across the nuclear envelope pores. However, Pauly et al. (2000) showed by studying nuclear Ca2+ signaling that elevations in the extranuclear Ca2+ concentration do not induce an automatic increase of nuclear [Ca2+] as it could be expected. Hence Ca2+ does not freely diffuse across the nuclear envelop pores, indicating that its transport is finely regulated. Then it becomes evident that we should now consider the nucleus as a key component of cell signaling processes leading to the regulation of specific sets of genes. The aim of this topic was to point out how nuclear post-translational modifications (PTMs) play fundamental roles in the signaling pathways initiated in response to environmental changes. Two major points were assessed. First, different papers clearly demonstrate that the nucleus is fully equipped to perform the main PTMs: (de)phosphorylation (Bigeard and Hirt; Krysan and Colcombet), (de)acetylation (Luo et al.; Fül et al.; Ramirez-Prado et al.), oxidoreduction (Martins et al.) or SUMOylation/ubiquitination (Mazur et al.; Serrano et al.). Hence the nucleus can easily integrate a complex network of second messengers including changes in Ca2+ concentration, reactive oxygen species or nitric oxide. Martins et al. nicely exemplified how changes in the nuclear redox status regulate fundamental processes such as cell cycle, protein transport or transcription via S-nitrosylation or S-glutationylation. Activation of nuclear PTMs can also be achieved by the translocation of enzymes which are both substrates and effectors of these PTMs. This is the case for mitogen-activated protein kinases (MAPKs) that in some specific contexts, translocate from the cytosol to the nucleus upon their activation by their corresponding MAPK kinases (Bigeard and Hirt). Relocation of proteins in response to or through PTMs can also be considered at the intranuclear level. Hence in response to SUMO conjugation several Arabidopsis transcription factors were shown to be re-localized in certain nuclear foci (Mazur et al.). PTMs can also affect the behavior of nuclear proteins and in fine their activity. Serrano et al. highlight how the ubiquitin-proteasome system contributes to the nuclear proteome plasticity. Focusing on E3-Ub-ligases, they illustrate how these enzymes attenuate the signaling pathway once the stress has ceased and how they control the homeostasis of nuclear proteins (transcription factors, immune receptors). The second major point of this topic concerns the target proteins of these PTMs. Of course histones are a piece of choice. The review by Ramirez-Prado et al. illustrates how removing or adding marks (phosphorylation, acetylation, methylation, or ubiquitination) on specific histone lysine residues associated to defense genes (WRKYs, pathogenesis-related proteins, etc.) mostly under the control of salicylic acid or jasmonic acid/ethylene signaling pathways, will control the outcome of the plant-microorganism interaction. A second interesting aspect in this review is the illustration of how pathogens manipulate the chromatin regulatory network of the host to achieve their infection process through for example the production of toxins inhibiting histone deacetylases (HDACs), leading to plant susceptibility. PTMs on histones are also of major importance in the response to abiotic stresses. Luo et al reviewed how HDACs, by deacetylating specific lysine residues (mainly H3K9, H3K14, and H4K15) of specific genes regulate responses to salt, drought, cold or heat. However, chromatin remodeling and in fine regulation of gene expression is not only linked to histone modifications. Fül et al. as a perspective in this topic remind us that subunits of key chromatin remodelers (such as MED12, MED13, and MED19A) or transcription factors like Yin Yang 1 in the response to abscisic acid are also targeted and regulated by lysine deacetylases. Hence lysine (de)acetylation regulates gene expression by acting on histones, but also on the whole transcriptional machinery. In conclusion this topic clearly illustrates the diversity of nuclear PTMs, the crosstalks between some of them, and finally their major roles in the regulation of gene expression. A first fascinating challenge is now to decipher at the molecular level the ways cells are using to translocate signals from cytoplasm to the nucleus that regulate nuclear PTMs. A second one is to go further in the characterization of their target proteins: as it is now nicely exemplified by the interplay of histone marks in epigenetics, this is the sine qua non condition to fully understand the power of nuclear PTMs. AU - Bourque, S.* AU - Lindermayr, C. AU - Mazars, C.* C1 - 55546 C2 - 46206 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland SP - 104 TI - Editorial: Post-translational modifications in plant nuclear signaling: Novel insights into responses to environmental changes. JO - Front. Plant Sci. VL - 10 PB - Frontiers Media Sa PY - 2019 SN - 1664-462X ER - TY - JOUR AB - The outcome of competition for nitrogen (N) between native and invasive tree species is a major concern when considering increasing anthropogenic N deposition. Our study investigated whether three native (i.e., Fagus sylvatica, Quercus robur, and Pinus sylvestris) and two invasive woody species (i.e., Prunus serotina and Robinia pseudoacacia) showed different responses regarding morphological and physiological parameters (i.e., biomass and growth indices, inorganic vs. organic N acquisition strategies, and N allocation to N pools) depending on the identity of the competing species, and whether these responses were mediated by soil N availability. In a greenhouse experiment, tree seedlings were planted either single or in native-invasive competition at low and high soil N availability. We measured inorganic and organic N acquisition using 15 N labeling, total biomass, growth indices, as well as total soluble amino acid-N and protein-N levels in the leaves and fine roots of the seedlings. Our results indicate that invasive species have a competitive advantage via high growth rates, whereas native species could avoid competition with invasives via their higher organic N acquisition suggesting a better access to organic soil N sources. Moreover, native species responded to competition with distinct species- and parameter-specific strategies that were partly mediated by soil N availability. Native tree seedlings in general showed a stronger response to invasive P. serotina than R. pseudoacacia, and their strategies to cope with competition reflect the different species’ life history strategies and physiological traits. Considering the responses of native and invasive species, our results suggest that specifically Q. robur seedlings have a competitive advantage over those of R. pseudoacacia but not P. serotina. Furthermore, native and invasive species show stronger responses to higher soil N availability under competition compared to when growing single. In conclusion, our study provides insights into the potential for niche differentiation between native and invasive species by using different N forms available in the soil, the combined effects of increased soil N availability and competition on tree seedling N nutrition, as well as the species-specific nature of competition between native and invasive tree seedlings which could be relevant for forest management strategies. AU - Bueno, A.* AU - Pritsch, K. AU - Simon, J.* C1 - 55839 C2 - 46612 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Species-specific outcome in the competition for nitrogen between invasive and native tree seedlings. JO - Front. Plant Sci. VL - 10 PB - Frontiers Media Sa PY - 2019 SN - 1664-462X ER - TY - JOUR AU - Csiszár, J.* AU - Hecker, A.* AU - Labrou, N.E.* AU - Schröder, P. AU - Riechers, D.E.* C1 - 57326 C2 - 47693 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Editorial: Plant glutathione transferases: Diverse, multi-tasking enzymes with yet-to-be discovered functions. JO - Front. Plant Sci. VL - 10 PB - Frontiers Media Sa PY - 2019 SN - 1664-462X ER - TY - JOUR AB - Plant-pathogen interactions have been widely studied, but mostly from the site of the plant secondary defense. Less is known about the effects of pathogen infection on plant primary metabolism. The possibility to transform a fluorescing protein into prokaryotes is a promising phenotyping tool to follow a bacterial infection in plants in a noninvasive manner. In the present study, virulent and avirulent Pseudomonas syringae strains were transformed with green fluorescent protein (GFP) to follow the spread of bacteria in vivo by imaging Pulse-Amplitude-Modulation (PAM) fluorescence and conventional binocular microscopy. The combination of various wavelengths and filters allowed simultaneous detection of GFP-transformed bacteria, PAM chlorophyll fluorescence, and phenolic fluorescence from pathogen-infected plant leaves. The results show that fluorescence imaging allows spatiotemporal monitoring of pathogen spread as well as phenolic and chlorophyll fluorescence in situ, thus providing a novel means to study complex plant-pathogen interactions and relate the responses of primary and secondary metabolism to pathogen spread and multiplication. The study establishes a deeper understanding of imaging data and their implementation into disease screening. AU - Hupp, S.* AU - Rosenkranz, M. AU - Bonfig, K.* AU - Pandey, C.* AU - Roitsch, T.* C1 - 57257 C2 - 47635 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Noninvasive phenotyping of plant-pathogen interaction: Consecutive in situ imaging of fluorescing Pseudomonas syringae, plant phenolic fluorescence, and chlorophyll fluorescence in Arabidopsis leaves. JO - Front. Plant Sci. VL - 10 PB - Frontiers Media Sa PY - 2019 SN - 1664-462X ER - TY - JOUR AB - Markers linked to agronomic traits are of the prerequisite for molecular breeding. Genotyping-by-sequencing (GBS) data enables to detect small polymorphisms including single nucleotide polymorphisms (SNPs) and short insertions or deletions (InDels) that can be used, for instance, for marker-assisted selection, population genetics, and genome-wide association studies (GWAS). Here, we aim at detecting large chromosomal modifications in barley and wheat based on GBS data. These modifications could be duplications, deletions, substitutions including introgressions as well as alterations of DNA methylation. We demonstrate that GBS coverage analysis is capable to detect Hordeum vulgare/Hordeum bulbosum introgression lines. Furthermore, we identify large chromosomal modifications in barley and wheat collections. Hence, large chromosomal modifications, including introgressions and copy number variations (CNV), can be detected easily and can be used as markers in research and breeding without additional wet-lab experiments. AU - Keilwagen, J.* AU - Lehnert, H.* AU - Berner, T.* AU - Beier, S.* AU - Scholz, U.* AU - Himmelbach, A.* AU - Stein, N.* AU - Badaeva, E.D.* AU - Lang, D. AU - Kilian, B.* AU - Hackauf, B.* AU - Perovic, D.* C1 - 57046 C2 - 47510 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Detecting large chromosomal modifications using short read data from genotyping-by-sequencing. JO - Front. Plant Sci. VL - 10 PB - Frontiers Media Sa PY - 2019 SN - 1664-462X ER - TY - JOUR AU - Millan, R.* AU - Schröder, P. AU - Saebo, A.* C1 - 55837 C2 - 46611 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland TI - Editorial: Options for transition of land towards intensive and sustainable agricultural systems. JO - Front. Plant Sci. VL - 10 PB - Frontiers Media Sa PY - 2019 SN - 1664-462X ER - TY - JOUR AU - Benckiser, G.* AU - Hartmann, A. AU - Kumar, K.G.* AU - Honermeier, B.* C1 - 53929 C2 - 45101 CY - Po Box 211, 1000 Ae Amsterdam, Netherlands TI - Editorial: Plant-microbe-insect interaction: Source for bio-fertilizers, bio-medicines and agent research. JO - Front. Plant Sci. VL - 9 PB - Elsevier Science Bv PY - 2018 SN - 1664-462X ER - TY - JOUR AB - Plant glutathione S-transferases (GSTs) are ubiquitous and multifunctional enzymes encoded by large gene families. A characteristic feature of genes is their high inducibility by a wide range of stress conditions including biotic stress. Early studies on the role of GSTs in plant biotic stress showed that certain genes are specifically up-regulated by microbial infections. Later numerous transcriptome-wide investigations proved that distinct groups of s are markedly induced in the early phase of bacterial, fungal and viral infections. Proteomic investigations also confirmed the accumulation of multiple GST proteins in infected plants. Furthermore, functional studies revealed that overexpression or silencing of specific can markedly modify disease symptoms and also pathogen multiplication rates. However, very limited information is available about the exact metabolic functions of disease-induced GST isoenzymes and about their endogenous substrates. The already recognized roles of GSTs are the detoxification of toxic substances by their conjugation with glutathione, the attenuation of oxidative stress and the participation in hormone transport. Some GSTs display glutathione peroxidase activity and these GSTs can detoxify toxic lipid hydroperoxides that accumulate during infections. GSTs can also possess ligandin functions and participate in the intracellular transport of auxins. Notably, the expression of multiple is massively activated by salicylic acid and some GST enzymes were demonstrated to be receptor proteins of salicylic acid. Furthermore, induction of genes or elevated GST activities have often been observed in plants treated with beneficial microbes (bacteria and fungi) that induce a systemic resistance response (ISR) to subsequent pathogen infections. Further research is needed to reveal the exact metabolic functions of GST isoenzymes in infected plants and to understand their contribution to disease resistance. AU - Gullner, G.* AU - Komives, T.* AU - Király, L.* AU - Schröder, P. C1 - 55049 C2 - 46029 CY - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland SP - 1836 TI - Glutathione s-transferase enzymes in plant-pathogen interactions. JO - Front. Plant Sci. VL - 871 PB - Frontiers Media Sa PY - 2018 SN - 1664-462X ER - TY - JOUR AB - The branched-chain amino acid (BCAA) related 2-hydroxy carboxylic acid isoleucic acid (ILA) enhances salicylic acid-mediated pathogen defense in Arabidopsis thaliana. ILA has been identified in A. thaliana as its glucose conjugate correlated with the activity of the small-molecule glucosyltransferase UGT76B1, which can glucosylate both salicylic acid and ILA in vitro. However, endogenous levels of the ILA aglycon have not yet been determined in planta. To quantify ILA as well as the related leucic acid (LA) and valic acid (VA) in plant extracts, a sensitive method based on the derivatization of small carboxylic acids by silylation and gas chromatography–mass spectrometric analysis was developed. ILA was present in all species tested including several monocotyledonous and dicotyledonous plants as well as broadleaf and coniferous trees, whereas LA and VA were only detectable in a few species. In A. thaliana both ILA and LA were found. However, their levels varied during plant growth and in root vs. leaves. ILA levels were higher in 2-week-old leaves and decreased in older plants, whereas LA exhibited a reverted accumulation pattern. Roots displayed higher ILA and LA levels compared to leaves. ILA was inversely related to UGT76B1 expression level indicating that UGT76B1 glucosylates ILA in planta. In contrast, LA was not affected by the expression of UGT76B1. To address the relation of both 2-hydroxy acids to plant defense, we studied ILA and LA levels upon infection by Pseudomonas syringae. LA abundance remained unaffected, whereas ILA was reduced. This change suggests an ILA-related attenuation of the salicylic acid response. Collectively, the BCAA-related ILA and LA differentially accumulated in Arabidopsis, supporting a specific role and regulation of the defense-modulating small-molecule ILA among these 2-hydroxy acids. The new sensitive method will pave the way to further unravel their role in plants. AU - Maksym, R.P. AU - Ghirardo, A. AU - Zhang, W. AU - von Saint Paul, V. AU - Lange, B. AU - Geist, B. AU - Hajirezaei, M.-R.* AU - Schnitzler, J.-P. AU - Schäffner, A. C1 - 53656 C2 - 44780 CY - Elsevier House, Brookvale Plaza, East Park Shannon, Co, Clare, 00000, Ireland SP - 766 TI - The defense-related isoleucic acid differentially accumulates in arabidopsis among branched-chain amino acid-related 2-hydroxy carboxylic acids. JO - Front. Plant Sci. VL - 9 PB - Elsevier Ireland Ltd PY - 2018 SN - 1664-462X ER - TY - JOUR AB - Plants like winter wheat are known for their insufficient N uptake between sowing and the following growing season. Especially after N-rich crops like oilseed rape or field bean, nitrogen retention of the available soil N can be poor, and the risk of contamination of the hydrosphere with nitrate (NO3-) and the atmosphere with nitrous oxide (N2O) is high. Therefore, novel strategies are needed to preserve these unused N resources for subsequent agricultural production. High organic carbon soil amendments (HCA) like wheat straw promote microbial N immobilization by stimulating microbes to take up N from soil. In order to test the suitability of different HCA for immobilization of excess N, we conducted a laboratory incubation experiment with soil columns, each containing 8 kg of sandy loam of an agricultural Ap horizon. We created a scenario with high soil mineral N content by adding 150 kg NH4+-N ha-1 to soil that received either wheat straw, spruce sawdust or lignin at a rate of 4.5 t C ha-1, or no HCA as control. Wheat straw turned out to be suitable for fast immobilization of excess N in the form of microbial biomass N (up to 42 kg N ha-1), followed by sawdust. However, under the experimental conditions this effect weakened over a few weeks, finally ranging between 8 and 15 kg N ha-1 immobilized in microbial biomass in the spruce sawdust and wheat straw treatment, respectively. Pure lignin did not stimulate microbial N immobilization. We also revealed that N immobilization by the remaining straw and sawdust HCA material in the soil had a greater importance for storage of excess N (on average 24 kg N ha-1) than microbial N immobilization over the 4 months. N fertilization and HCA influenced the abundance of ammonia oxidizing bacteria and archaea as the key players for nitrification, as well as the abundance of denitrifiers. Soil with spruce sawdust emitted more N2O compared to soil with wheat straw, which in relation released more CO2, resulting in a comparable overall global warming potential. However, this was counterbalanced by advantages like N immobilization and mitigation of potential NO3- losses. AU - Reichel, R.* AU - Wei, J.* AU - Islam, M.S.* AU - Schmid, C. AU - Wissel, H.* AU - Schröder, P. AU - Schloter, M. AU - Brüggemann, N.* C1 - 53930 C2 - 45098 CY - Po Box 211, 1000 Ae Amsterdam, Netherlands TI - Potential of wheat straw, spruce sawdust, and lignin as high organic carbon soil amendments to improve agricultural nitrogen retention capacity: An incubation study. JO - Front. Plant Sci. VL - 9 PB - Elsevier Science Bv PY - 2018 SN - 1664-462X ER - TY - JOUR AB - Induction of plant resistance against pathogens by defense elicitors constitutes an attractive strategy to reduce the use of fungicides in crop protection. However, all elicitors do not systematically confer protection against pathogens. Elicitor-induced resistance (IR) thus merits to be further characterized in order to understand what makes an elicitor efficient. In this study, the oligosaccharidic defense elicitors H13 and PS3, respectively, ineffective and effective to trigger resistance of grapevine leaves against downy mildew, were used to compare their effect on the global leaf metabolism. Ultra high resolution mass spectrometry (FT-ICR-MS) analysis allowed us to obtain and compare the specific metabolic fingerprint induced by each elicitor and to characterize the associated metabolic pathways. Moreover, erythritol phosphate was identified as a putative marker of elicitor-IR. AU - Adrian, M.V.* AU - Lucio, M. AU - Roullier-Gall, C. AU - Héloir, M.C.* AU - Trouvelot, S.* AU - Daire, X.* AU - Kanawati, B. AU - Lemaître-Guillier, C.* AU - Poinssot, B.* AU - Gougeon, R.* AU - Schmitt-Kopplin, P. C1 - 50546 C2 - 42626 CY - Lausanne TI - Metabolic fingerprint of ps3-induced resistance of grapevine leaves against plasmopara viticola revealed differences in elicitor-triggered defenses. JO - Front. Plant Sci. VL - 8 PB - Frontiers Media Sa PY - 2017 SN - 1664-462X ER - TY - JOUR AB - In this study, we investigated the impact of different land use intensities (LUI) on the root-associated microbiome of Dactylis glomerata (orchardgrass). For this purpose, eight sampling sites with different land use intensity levels but comparable soil properties were selected in the southwest of Germany. Experimental plots covered land use levels from natural grassland up to intensively managed meadows. We used 16S rRNA gene based barcoding to assess the plant-associated community structure in the endosphere, rhizosphere and bulk soil of D. glomerata. Samples were taken at the reproductive stage of the plant in early summer. Our data indicated that roots harbor a distinct bacterial community, which clearly differed from the microbiome of the rhizosphere and bulk soil. Our results revealed Pseudomonadaceae, Enterobacteriaceae and Comamonadaceae as the most abundant endophytes independently of land use intensity. Rhizosphere and bulk soil were dominated also by Proteobacteria, but the most abundant families differed from those obtained from root samples. In the soil, the effect of land use intensity was more pronounced compared to root endophytes leading to a clearly distinct pattern of bacterial communities under different LUI from rhizosphere and bulk soil vs. endophytes. Overall, a change of community structure on the plant–soil interface was observed, as the number of shared OTUs between all three compartments investigated increased with decreasing land use intensity. Thus, our findings suggest a stronger interaction of the plant with its surrounding soil under low land use intensity. Furthermore, the amount and quality of available nitrogen was identified as a major driver for shifts in the microbiome structure in all compartments. AU - Estendorfer, J. AU - Stempfhuber, B. AU - Haury, P. AU - Vestergaard, G. AU - Rillig, M.C.* AU - Joshi, J.* AU - Schröder, P. AU - Schloter, M. C1 - 51459 C2 - 43219 CY - Lausanne TI - The influence of land use intensity on the plant-associated microbiome of Dactylis glomerata L. JO - Front. Plant Sci. VL - 8 PB - Frontiers Media Sa PY - 2017 SN - 1664-462X ER - TY - JOUR AU - Kasten, D. AU - Durner, J. AU - Gaupels, F. C1 - 50530 C2 - 42508 CY - Lausanne TI - Gas alert: The NO2 pitfall during NO fumigation of plants. JO - Front. Plant Sci. VL - 8 PB - Frontiers Media Sa PY - 2017 SN - 1664-462X ER - TY - JOUR AB - Many studies have been pointing to a high diversity of bacteria associated to legume root nodules. Even though most of these bacteria do not form nodules with legumes themselves, it was shown that they might enter infection threads when co-inoculated with rhizobial strains. The aim of this work was to describe the diversity of bacterial communities associated with cowpea (Vigna unguiculata L. Walp) root nodules using 16S rRNA gene amplicon sequencing, regarding the factors plant genotype and soil type. As expected, Bradyrhizobium was the most abundant genus of the detected genera. Furthermore, we found a high bacterial diversity associated to cowpea nodules; OTUs related to the genera Enterobacter, Chryseobacterium, Sphingobacterium, and unclassified Enterobacterfacea were the most abundant. The presence of these groups was significantly influenced by the soil type and, to a lesser extent, plant genotype. Interestingly, OTUs assigned to Chryseobacterium were highly abundant, particularly in samples obtained from an Ultisol soil. We confirmed their presence in root nodules and assessed their diversity using a target isolation approach. Though their functional role still needs to be addressed, we postulate that Chryseobacterium strains might help cowpea plant to cope with salt stress in semi-arid regions. AU - Leite, J.* AU - Fischer, D. AU - Rouws, L.F.M.* AU - Fernandes-Junior, P.* AU - Hofmann, A. AU - Kublik, S. AU - Schloter, M. AU - Xavier, G.R.* AU - Radl, V. C1 - 50498 C2 - 42381 CY - Lausanne TI - Cowpea nodules harbor non-rhizobial bacterial communities that are shaped by soil type rather than plant genotype. JO - Front. Plant Sci. VL - 7 PB - Frontiers Media Sa PY - 2017 SN - 1664-462X ER - TY - JOUR AB - Endophytes are microorganisms colonizing plant internal tissues. They are ubiquitously associated with plants and play an important role in plant growth and health. In this work, we grew five modern cultivars of barley in axenic systems using sterile sand mixture as well as in greenhouse with natural soil. We characterized the potentially active microbial communities associated with seeds and roots using rRNA based amplicon sequencing. The seeds of the different cultivars share a great part of their microbiome, as we observed a predominance of a few bacterial OTUs assigned to Phyllobacterium, Paenibacillus, and Trabusiella. Seed endophytes, particularly members of the Enterobacteriacea and Paenibacillaceae, were important members of root endophytes in axenic systems, where there were no external microbes. However, when plants were grown in soil, seed endophytes became less abundant in root associated microbiome. We observed a clear enrichment of Actinobacteriacea and Rhizobiaceae, indicating a strong influence of the soil bacterial communities on the composition of the root microbiome. Two OTUs assigned to Phyllobacteriaceae were found in all seeds and root samples growing in soil, indicating a relationship between seed-borne and root associated microbiome in barley. Even though the role of endophytic bacteria remains to be clarified, it is known that many members of the genera detected in our study produce phytohormones, shape seedling exudate profile and may play an important role in germination and establishment of the seedlings. AU - Yang, L. AU - Danzberger, J. AU - Schöler, A. AU - Schröder, P. AU - Schloter, M. AU - Radl, V. C1 - 51421 C2 - 43143 CY - Lausanne TI - Dominant groups of potentially active bacteria shared by barley seeds become less abundant in root associated microbiome. JO - Front. Plant Sci. VL - 8 PB - Frontiers Media Sa PY - 2017 SN - 1664-462X ER - TY - JOUR AU - Astier, J. AU - Loake, G.* AU - Velikova, V.B.* AU - Gaupels, F. C1 - 50031 C2 - 41990 CY - Lausanne TI - Editorial: Interplay between NO signaling, ROS, and the antioxidant system in plants. JO - Front. Plant Sci. VL - 7 PB - Frontiers Media Sa PY - 2016 SN - 1664-462X ER - TY - JOUR AB - This mini-review summarizes the available data of the air pollutants NO2 and ozone on allergenic pollen from different plant species, focusing on potentially allergenic components of the pollen, such as allergen content, protein release, IgE-binding, or protein modification. Various in vivo and in vitro studies on allergenic pollen are shown and discussed. AU - Frank, U. AU - Ernst, D. C1 - 47952 C2 - 39832 CY - Lausanne TI - Effects of NO2 and ozone on pollen allergenicity. JO - Front. Plant Sci. VL - 7 PB - Frontiers Media Sa PY - 2016 SN - 1664-462X ER - TY - JOUR AB - Cucurbits developed the unique extrafascicular phloem (EFP) as a defensive structure against herbivorous animals. Mechanical leaf injury was previously shown to induce a systemic wound response in the EFP of pumpkin (Cucurbita maxima). Here, we demonstrate that the phloem antioxidant system and protein modifications by NO are strongly regulated during this process. Activities of the central antioxidant enzymes dehydroascorbate reductase, glutathione reductase and ascorbate reductase were rapidly down-regulated at 30 min with a second minimum at 24 h after wounding. As a consequence levels of total ascorbate and glutathione also decreased with similar bi-phasic kinetics. These results hint toward a wound-induced shift in the redox status of the EFP. Nitric oxide (NO) is another important player in stress-induced redox signaling in plants. Therefore, we analyzed NO-dependent protein modifications in the EFP. Six to forty eight hours after leaf damage total S-nitrosothiol content and protein S-nitrosylation were clearly reduced, which was contrasted by a pronounced increase in protein tyrosine nitration. Collectively, these findings suggest that NO-dependent S-nitrosylation turned into peroxynitrite-mediated protein nitration upon a stress-induced redox shift probably involving the accumulation of reactive oxygen species within the EFP. Using the biotin switch assay and anti-nitrotyrosine antibodies we identified 9 candidate S-nitrosylated and 6 candidate tyrosine-nitrated phloem proteins. The wound-responsive Phloem Protein 16-1 (PP16-1) and Cyclophilin 18 (CYP18) as well as the 26.5 kD isoform of Phloem Protein 2 (PP2) were amenable to both NO modifications and could represent important redox-sensors within the cucurbit EFP. We also found that leaf injury triggered the systemic accumulation of cyclic guanosine monophosphate (cGMP) in the EFP and discuss the possible function of this second messenger in systemic NO and redox signaling within the EFP. AU - Gaupels, F. AU - Furch, A.C.* AU - Zimmermann, M.R.* AU - Chen, F.* AU - Kaever, V.* AU - Buhtz, A.* AU - Kehr, J.* AU - Sarioglu, H. AU - Kogel, K.H.* AU - Durner, J. C1 - 47948 C2 - 39772 CY - Lausanne TI - Systemic induction of NO-, redox-, and cGMP signaling in the pumpkin extrafascicular phloem upon local leaf wounding. JO - Front. Plant Sci. VL - 7 PB - Frontiers Media Sa PY - 2016 SN - 1664-462X ER - TY - JOUR AB - [This corrects the article on p. 154 in vol. 7, PMID: 26904092.]. AU - Gaupels, F. AU - Furch, A.C.U.* AU - Zimmermann, M.R.* AU - Chen, F.* AU - Kaever, V.* AU - Buhtzt, A.* AU - Kehr, J.* AU - Sarioglu, H. AU - Koger, K.* AU - Durner, J. C1 - 48175 C2 - 41086 CY - Lausanne TI - Corrigendum: Systemic induction of NO-, Redox-, and cGMP signaling in the pumpkin extrafascicular phloem upon local leaf wounding (vol 7, 154, 2016). JO - Front. Plant Sci. VL - 7 PB - Frontiers Media Sa PY - 2016 SN - 1664-462X ER - TY - JOUR AB - In plants, nitric oxide (NO)-mediated 3′, 5′-cyclic guanosine monophosphate (cGMP) synthesis plays an important role during pathogenic stress response, stomata closure upon osmotic stress, the development of adventitious roots and transcript regulation. The NO-cGMP dependent pathway is well characterized in mammals. The binding of NO to soluble guanylate cyclase enzymes (GCs) initiates the synthesis of cGMP from guanosine triphosphate. The produced cGMP alters various cellular responses, such as the function of protein kinase activity, cyclic nucleotide gated ion channels and cGMP-regulated phosphodiesterases. The signal generated by the second messenger is terminated by 3′, 5′-cyclic nucleotide phosphodiesterase (PDEs) enzymes that hydrolyze cGMP to a non-cyclic 5′-guanosine monophosphate. To date, no homologues of mammalian cGMP-synthesizing and degrading enzymes have been found in higher plants. In the last decade, six receptor proteins from Arabidopsis thaliana have been reported to have guanylate cyclase activity in vitro. Of the six receptors, one was shown to be a NO dependent guanylate cyclase enzyme (NOGC1). However, the role of these proteins in planta remains to be elucidated. Enzymes involved in the degradation of cGMP remain elusive, albeit, PDE activity has been detected in crude protein extracts from various plants. Additionally, several research groups have partially purified and characterized PDE enzymatic activity from crude protein extracts. In this review, we focus on presenting advances toward the identification of enzymes involved in the cGMP metabolism pathway in higher plants. AU - Gross, I. AU - Durner, J. C1 - 48629 C2 - 41239 CY - Lausanne TI - In search of enzymes with a role in 3′, 5′-cyclic guanosine monophosphate metabolism in plants. JO - Front. Plant Sci. VL - 7 PB - Frontiers Media Sa PY - 2016 SN - 1664-462X ER - TY - JOUR AB - Quorum sensing auto-inducers of the N-acyl homoserine lactone (AHL) type produced by Gram-negative bacteria have different effects on plants including stimulation on root growth and/or priming or acquirement of systemic resistance in plants. In this communication the influence of AHL production of the plant growth promoting endophytic rhizosphere bacterium Acidovorax radicis N35 on barley seedlings was investigated. A. radicis N35 produces 3-hydroxy-C10-homoserine lactone (3-OH-C10-HSL) as the major AHL compound. To study the influence of this QS autoinducer on the interaction with barley, the ara/-biosynthesis gene was deleted. The comparison of inoculation effects of the A. radicis N35 wild type and the aral mutant resulted in remarkable differences. While the N35 wild type colonized plant roots effectively in microcolonies, the aral mutant occurred at the root surface as single cells. Furthermore, in a mixed inoculum the wild type was much more prevalent in colonization than the aral mutant documenting that the aral mutation affected root colonization. Nevertheless, a significant plant growth promoting effect could be shown after inoculation of barley with the wild type and the aral mutant in soil after 2 months cultivation. While A. radicis N35 wild type showed only a very weak induction of early defense responses in plant RNA expression analysis, the aral mutant caused increased expression of flavonoid biosynthesis genes. This was corroborated by the accumulation of several flavonoid compounds such as saponarin and lutonarin in leaves of root inoculated barley seedlings. Thus, although the exact role of the flavonoids in this plant response is not clear yet, it can be concluded, that the synthesis of AHLs by A. radicis has implications on the perception by the host plant barley and thereby contributes to the establishment and function of the bacteria-plant interaction. AU - Han, S. AU - Li, D. AU - Trost, E. AU - Mayer, K.F.X. AU - Vlot, A.C. AU - Heller, W. AU - Schmid, M. AU - Hartmann, A. AU - Rothballer, M. C1 - 50230 C2 - 39919 CY - Lausanne TI - Systemic responses of Barley to the 3-hydroxy-decanoyl-homoserine lactone producing plant beneficial endophyte acidovorax radicis N35. JO - Front. Plant Sci. VL - 7 PB - Frontiers Media Sa PY - 2016 SN - 1664-462X ER - TY - JOUR AB - Nitric oxide (NO) has emerged as a signaling molecule in plants being involved in diverse physiological processes like germination, root growth, stomata closing and response to biotic and abiotic stress. S-nitrosoglutathione (GSNO) as a biological NO donor has a very important function in NO signaling since it can transfer its NO moiety to other proteins (trans-nitrosylation). Such trans-nitrosylation reactions are equilibrium reactions and depend on GSNO level. The breakdown of GSNO and thus the level of S-nitrosylated proteins are regulated by GSNO-reductase (GSNOR). In this way, this enzyme controls S-nitrosothiol levels and regulates NO signaling. Here we report that Arabiclopsis thahana GSNOR activity is reversibly inhibited by H2O2 in vitro and by paraquat-induced oxidative stress in vivo. Light scattering analyses of reduced and oxidized recombinant GSNOR demonstrated that GSNOR proteins form dimers under both reducing and oxidizing conditions. Moreover, mass spectrometric analyses revealed that H2O2-treatment increased the amount of oxidative modifications on Zn2+-coordinating Cys47 and Cys177. Inhibition of GSNOR results in enhanced levels of S-nitrosothiols followed by accumulation of glutathione. Moreover, transcript levels of redox-regulated genes and activities of glutathione-dependent enzymes are increased in gsnor-ko plants, which may contribute to the enhanced resistance against oxidative stress. In sum, our results demonstrate that reactive oxygen species (ROS)dependent inhibition of GSNOR is playing an important role in activation of anti-oxidative mechanisms to damping oxidative damage and imply a direct crosstalk between ROS- and NO-signaling. AU - Kovacs, I. AU - Holzmeister, C. AU - Wirtz, M.* AU - Geerlof, A. AU - Fröhlich, T.* AU - Römling, G. AU - Kuruthukulangarakoola, G.T. AU - Linster, E.* AU - Hell, R.* AU - Arnold, G.J.* AU - Durner, J. AU - Lindermayr, C. C1 - 50038 C2 - 42043 CY - Lausanne TI - ROS-mediated inhibition of S-nitrosoglutathione reductase contributes to the activation of anti-oxidative mechanisms. JO - Front. Plant Sci. VL - 7 PB - Frontiers Media Sa PY - 2016 SN - 1664-462X ER - TY - JOUR AB - Inducing resistance in plants by the application of elicitors of defense reactions is an attractive plant protection strategy, particularly for grapevine (Vitis vinifera), which is susceptible to severe fungal diseases. Although induced resistance (IR) can be successful under controlled conditions, in most cases, IR is not sufficiently effective for practical disease control under outdoor conditions. Progress in the application of IR requires a better understanding of grapevine defense mechanisms and the ability to monitor defense markers to identify factors, such as physiological and environmental factors, that can impact IR in the vineyard. Volatile organic compounds (VOCs) are well-known plant defense compounds that have received little or no attention to date in the case of grape-pathogen interactions. This prompted us to investigate whether an elicitor, the sulfated laminarin (PS3), actually induces the production of VOCs in grapevine. An online analysis (proton-transfer-reaction quadrupole mass spectrometry) of VOC emissions in dynamic cuvettes and passive sampling in gas-tight bags with solid-phase microextraction-GC-MS under greenhouse conditions showed that PS3 elicited the emission of VOCs. Some of them, such as (E,E)-α-farnesene, may be good candidates as biomarkers of elicitor-IR, whereas methyl salicylate appears to be a biomarker of downy mildew infection. A negative correlation between VOC emission and disease severity suggests a positive role of VOCs in grape defense against diseases. AU - Chalal, M.* AU - Winkler, J.B. AU - Gourrat, K.* AU - Trouvelot, S.* AU - Adrian, M.V.* AU - Schnitzler, J.-P. AU - Jamois, F.* AU - Daire, X.* C1 - 45112 C2 - 37214 CY - Lausanne TI - Sesquiterpene Volatile Organic Compounds (VOCs) are markers of elicitation by sulfated laminarine in grapevine. JO - Front. Plant Sci. VL - 6 PB - Frontiers Research Foundation PY - 2015 SN - 1664-462X ER - TY - JOUR AB - The APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily of transcription factors (TFs) regulates physiological, developmental and stress responses. Most of the AP2/ERF TFs belong to the ERF family in both dicotyledonous and monocotyledonous plants. ERFs are implicated in the responses to both biotic and abiotic stress and occasionally impart multiple stress tolerance. Studies have revealed that ERF gene function is conserved in dicots and monocots. Moreover, successful stress tolerance phenotypes are observed on expression in heterologous systems, making ERFs promising candidates for engineering stress tolerance in plants. In this review, we summarize the role of ERFs in general stress tolerance, including responses to biotic and abiotic stress factors, and endeavor to understand the cascade of ERF regulation resulting in successful signal-to-response translation in monocotyledonous plants. AU - Dey, S. AU - Vlot, A.C. C1 - 46758 C2 - 37792 CY - Lausanne TI - Ethylene responsive factors in the orchestration of stress responses in monocotyledonous plants. JO - Front. Plant Sci. VL - 6 PB - Frontiers Media Sa PY - 2015 SN - 1664-462X ER - TY - JOUR AB - Bacteria are able to communicate with each other and sense their environment in a population density dependent mechanism known as quorum sensing (QS). N-acyl- homoserine lactones (AHLs) are the QS signaling compounds of Gram-negative bacteria which are frequent colonizers of rhizospheres. While cross-kingdom signaling and AHL- dependent gene expression in plants has been confirmed, the responses of enzyme activities in the eukaryotic host upon AHLs are unknown. Since AHL are thought to be used as so-called plant boosters or strengthening agents, which might change their resistance toward radiation and/or xenobiotic stress, we have examined the plants pigment status and their antioxidative and detoxifying capacities upon AHL treatment. Because the yield of a crop plant should not be negatively influenced, we have also checked for growth and root parameters. We investigated the influence of three different AHLs, namely N-hexanoyl- (C6-HSL), N-octanoyl- (C8-HSL), and N-decanoyl- homoserine lactone (C10-HSL) on two agricultural crop plants. The AHL-effects on Hordeum vulgare (L.) as an example of a monocotyledonous crop and on the tropical leguminous crop plant Pachyrhizus erosus (L.) were compared. While plant growth and pigment contents in both plants showed only small responses to the applied AHLs, AHL treatment triggered tissue- and compound-specific changes in the activity of important detoxification enzymes. The activity of dehydroascorbate reductase in barley shoots after C10-HSL treatment for instance increased up to 384% of control plant levels, whereas superoxide dismutase activity in barley roots was decreased down to 23% of control levels upon C6-HSL treatment. Other detoxification enzymes reacted similarly within this range, with interesting clusters of positive or negative answers toward AHL treatment.In general the changes on the enzyme level were more severe in barley than in yam bean which might be due to the differentabilities of the plants to degrade AHLs to metabolites such as thehy droxy-or keto-form of the original compound. AU - Götz-Rösch, C. AU - Sieper, T. AU - Fekete, A. AU - Schmitt-Kopplin, P. AU - Hartmann, A. AU - Schröder, P. C1 - 44499 C2 - 36927 CY - Lausanne TI - Influence of bacterial N-acyl-homoserine lactones on growth parameters, pigments, antioxidative capacities and the xenobiotic phase II detoxification enzymes in barley and yam bean. JO - Front. Plant Sci. VL - 6 PB - Frontiers Research Foundation PY - 2015 SN - 1664-462X ER - TY - JOUR AU - Hartmann, A. AU - Schikora, A.* C1 - 46712 C2 - 37743 CY - Lausanne TI - Plant responses to bacterial quorum sensing molecules. JO - Front. Plant Sci. VL - 6 PB - Frontiers Media Sa PY - 2015 SN - 1664-462X ER - TY - JOUR AB - Carbamazepine is an antiepileptic and mood-stabilizing drug which is used widely in Europe and North America. In the environment, it is found as a persistent and recalcitrant contaminant, being one of the most prominent hazardous pharmaceuticals and personal care products in effluents of wastewater treatment plants. Phragmites australis is one of the species with both, the highest potential of detoxification and phytoremediation. It has been used successfully in the treatment of industrial and municipal wastewater. Recently, the identification of endophytic microorganisms from different plant species growing in contaminated sites has provided a list of candidates which could be used as bio-inoculants for bioremediation of difficult compounds. In this study, Phragmites australis plants were exposed to 5 mg/L of carbamazepine. After 9 days the plants had removed 90% of the initial concentration. Endophytic bacteria were isolated from these plants and further characterized. Phylogenetic analysis based on 16S rDNA sequencing revealed that the majority of these isolates belong to three groups: Proteobacteria, Actinobacteria, and Bacteroidetes. Carbamazepine uptake and plant growth promoting (PGP) traits were analyzed among the isolates. Ninety percent of the isolates produce indole acetic acid (IAA) and all of them possess at least one of the PGP traits tested. One isolate identified as Chryseobacterium taeanense combines good carbamazepine uptake and all of the PGP traits. Rhizobium daejeonense can remove carbamazepine and produces 23 μg/mL of IAA. Diaphorobacter nitroreducens and Achromobacter mucicolens are suitable for carbamazepine removal while both, Pseudomonas veronii and Pseudomonas lini show high siderophore production and phosphate solubilization. Alone or in combination, these isolates might be applied as inoculates in constructed wetlands in order to enhance the phytoremediation of carbamazepine during wastewater treatment. AU - Sauvetre, A. AU - Schröder, P. C1 - 43517 C2 - 36633 CY - Lausanne TI - Uptake of carbamazepine by rhizomes and endophytic bacteria of Phragmites australis. JO - Front. Plant Sci. VL - 6 PB - Frontiers Research Foundation PY - 2015 SN - 1664-462X ER - TY - JOUR AB - Interference of pathogenic as well as symbiotic microbes with the innate immune response via their MAMPS is fundamental for microbe-host interactions. In addition, a multitude of microbial effector molecules are modulating or even initiating specific mutualistic activities in host plants. It is hypothesized, that quorum sensing molecules, like the N-acyl-homoserine lactones of Gram-negative bacteria, should be regarded as important players or modulators of host-bacteria interactions. Other known or still structurally unknown quorum sensing compounds may also serve as central functional glue between root-colonizing / endophytic bacteria and their hosts. While the interactions of plants with pure/single effectors were studied in some detail, the interaction network with other elicitors and effectors of plant responses is still largely unexplored. Functional interaction studies of holobiotic plant systems, including the plant host and its associated microbes, may result in a more profound understanding of the complicated social network of basic innate immune responses with specific effector molecules, if quorum sensing compounds of endophytic bacteria are integrated. Plant - microbiome interactions in the light of the holobiontic concept Higher organisms evolved in the omnipresence of microbes, which could be of pathogenic or symbiotic nature. A framework of response patterns evolved which is known as innate immunity. A major part of this response is the recognition of microbial-associated molecular patterns (MAMP) such as chitin or lipochitooligosaccharides, peptidoglycan, lipopolysaccharides or flagellum structures and the initiation of efficient plant defence reactions (Janeway and Medzhitov, 2002; Jones and Dangl, 2006). However, there are many plant-associated endophytic bacteria known, which are living within plants without triggering persistent and apparent defence responses or visibly do not harm the plant. In some cases, even a stimulation of plant growth due to the presence of specific players within the plant microbiome was reported (Turner et al., 2013). It is now generally accepted, that plant performance and activities can only be characterized and understood completely, if the “holobiont”, the plant plus the intimately associated microbiota, is considered (Zilber-Rosenberg et al., 2008). The evolutionary advantage of an integrated holobiontic system is characterized by a much better adaptability and flexibility towards rapidly changing adverse environmental conditions. It is still mostly unknown, which particular plant genetic loci are controlling the interactions with the plant microbiome and which signals are steering this cooperativity. Mutualistic microbes are able to overcome or short-circuit plant defence responses to enable successful colonization of the host (Zamioudis and Pieterse, 2012; Alqueres et al., 2012). Beneficial associations with microbes other than mycorhiza or Rhizobia are also controlled by systemically regulated or autoregulated processes on top of the basic innate immunity response. The induction of systemic immunity responses like ISR (induced systemic resistance) by some beneficial rhizosphere bacteria or the SAR (systemic acquired resistance) response provoked by pathogens are results of multiple response cascades employed by the plant host to respond to microbial and other environmental interactions. However, the entire response network is by far not yet revealed. For example, bacteria-induced plant responses resulting in improved resistance towards pathogens can also be due to the perception of secondary metabolites, like the surfactin lipopeptide, produced by certain biocontrol Bacilli (Garcia-Gutiérrez et al., 2013) or volatile compounds of plant-associated microbes (Yi et al., 2010). The biocontrol activity of microbial inoculants is probably due to multiple effects of their secondary metabolites to achieve direct inhibition of the pathogenic counterpart as well as an increase of systemic resistance of the plant host. Bacterial quorum sensing molecules like N-acyl homoserine lactones modulate plant responses towards contact with bacteria It is hypothesized, that eukaryotic organisms developed ways to sense microbes in addition to the recognition of their MAMPs by their diffusible small molecules. A very ancient and basic feature of unicellular bacteria is their way of environmental sensing and social communication. In many Gram-negative bacteria the synthesis of autoinducers of the N-acyl-homoserine lactone (AHL) type is tightly regulated in response to cell density or the cell “quorum” (Eberl, 1999). These metabolites are released into the cellular environment to sense the quality of the ecological niche in terms of diffusion space and the density and distribution of their own population. This environmental sensing mechanism helps to adapt the regulation of their gene expression to the given conditions in their habitat and thus optimizes the fitness of the population. Therefore, the generally known term “quorum sensing” (QS) was supplemented by the more broadly defined concept of “efficiency sensing” (Hense et al., 2007). Since this optimization of in situ gene expression is of very basic importance, autoinducer QS-molecules are widespread among bacteria and have quite different molecular structures. N-acyl-homoserine lactones (AHL) are common in Gram-negative bacteria, while cyclic peptides as QS-signals are only to be found in Gram-positive bacteria. The detailed structure of the AHL-molecules can vary; the acyl side chain consists of 4 to 14 carbon atoms and may also contain double bonds. The C3-atom can be hydroxylated or oxidized to a carbonyl-carbon; thus, considerable information and quite different physicochemical properties can be present within these different AHL-structures. As is outlined below, also plants have obviously learned during their evolution to respond to these quorum sensing compounds in different specific ways. We speculate, that QS-compounds are early signals indicating that pathogens are in the surroundings to gather themselves for attack or that mutualists are about to interact with roots. The first demonstration of specific responses of a plant to bacterial N-acyl-homoserine lactones was demonstrated for the legume Medicago truncatula (Mathesius et al., 2003). AHLs from symbiotic (Sinorhizobium meliloti) or pathogenic (Pseudomonas aeruginosa) bacteria provoked at concentrations as low as nano- to micromolar significant changes in the accumulation of over 150 proteins. Auxin-responsive and flavonoid synthesis proteins were induced and also a secretion of plant metabolites that mimic quorum sensing compounds were found, which may have the potential to disrupt quorum sensing signalling by associated bacteria. In tomato plants, a specific induction of systemic resistance proteins after inoculation of the roots with C4- and C6-side chain AHL-producing Serratia liquefaciens MG1 was discovered independently (Hartmann et al., 2004; Schuhegger et al., 2006). The fungal leaf pathogen Alternaria alternata was much less effective, when S. liquefaciens MG 1 wild type had been inoculated to roots of tomato plants as compared to the AHL-negative mutant. It could be shown, that salicylic acid was increased as well as SA- and ethylene-dependent defence genes (i.e. PR1a) in MG1-inoculated plants. Furthermore, Serratia plymuthica HRO-C48, producing C4-/C6- and OHC4-/OHC6-homoserine lactones, is able to induce ISR-like systemic protection of bean and tomato plants against the fungal leaf pathogen Botrytis cinnera; this response was greatly reduced with mutants impaired in AHL-production (Liu et al., 2007; Pang et al., 2009). In contrast, Arabidopsis thaliana responds to short (C4- and C6-) N-acyl AHL-compounds in a different manner: C4- and C6- homoserine lactones alter the expression of selected hormonal regulated genes which results in changes of the plant´s hormone content, in particular an increased auxin / cytokinin ratio (von Rad et al., 2008). However, no systemic resistance response was found to be induced in A. thaliana when roots were stimulated with short side-chain AHLs. Ortiz-Castro et al. (2008) found that C10-homoserine lactone elicited developmental changes in the root system in Arabidopsis plants by altering the expression of cell division and differentiation-related genes. Furthermore, Liu et al. (2012) and Jin et al. (2012) demonstrated that the root stimulatory effect of C6- and C8- homoserine lactones in Arabidopsis plants is mediated through the G-protein coupled receptor encoded by AtGPA1. In mung bean, oxoC10-homoserine lactone activates auxin-induced adventitious root formation via H2O2- and NO-dependent cyclic GMP signaling (Bai et al., 2012). On the other hand, N-acyl-AHLs with C12- and C14- side chains induce systemic resistance to the obligate biotrophic fungus Golovinomyces orontii in A. thaliana and to Blumeria graminis f. sp. hordei in barley (Hordeum vulgare) (Schikora et al., 2011). This response is mediated through altered activation of AtMPK6. The mitogen-activated protein kinases AtMPK3 and AtMPK6 were stronger activated by the model elicitor flg22 in the presence of C12- or C14-AHL compounds which resulted in a higher expression of the defence-related transcription factors WRKY26 and WRKY29 as well as the PR1 gene (Schikora et al., 2011). Thus, AHLs with short and medium side lengths induce developmental effects on root architecture, while long side chain AHLs induce systemic resistance in A. thaliana (Schenk et al., 2012). Furthermore, it was shown, that better water soluble short side chain AHL-compounds are actively taken up into plant roots and transported along the roots into the shoot; in contrast, the lipophilic long acyl side chain AHLs are not transported in barley and A. thaliana. (Götz et al., 2007, von Rad et al., 2008, Sieper et al., 2014). However, no uptake was detected in the legume yam bean (Pachyrhizus erosus (L.) Urban) (Götz et al., 2007). The latter finding corroborates the report of Delalande et al. (2008) that legumes like Lotus corniculatus produce lactonases which degrade AHLs and prevents its uptake and transport. In barley, it could further be demonstrated that C8- and C10-AHLs are taken up in a cell energy dependent manner by ABC-transporters into the root and transported via the central cylinder into the shoot (Sieper et al., 2014). Interestingly, several plants have been demonstrated to produce AHL-mimic substances or to develop other activities influencing quorum sensing of plant associated bacteria (Gao et al., 2003; Bauer and Mathesius, 2004). Flavonoids released by legumes increase the expression of N-acyl-homoserine lactone synthesis genes in Rhizobia (Pérez-Montano et al., 2011): Indole acetic acid and cytokinin biosynthesis of Gypsophila was shown to influence QS, type III secretion system and gall formation activity by Pantoea plantarum (Chalupowicz et al., 2009). On the other hand, tobacco plants have been engineered to produce short- and long-side chain AHL-compounds which could be detected in substantial amounts at leaf and root surfaces as well as in soil (Scott et al., 2006). Constitutive expression of quorum sensing genes in transgenic tobacco plants leads to alteration in induced systemic resistance elicited by the rhizobacterium Serratia marcescens 90-166 (Ryu et al., 2013). Furthermore, transgenic tomato plants engineered to produce different AHL-compounds were demonstrated to alter the activity of plant growth promoting rhizobacteria and resulted e.g. in increased salt tolerance (Barriuso et al., 2008). We hypothesize, that quorum sensing in a plant-microbe holobiont system should be regarded in a bidirectional way with influences from the plant and the microbial partners. Uptake of AHL-compounds and specific perception of AHLs in animal cells were also studied intensively in recent years (Teplitski et al., 2011; Hartmann and Schikora, 2012). 3-oxo-C12-homoserine lactone (C12-AHL), the major AHL-compound of Pseudomonas aeruginosa, was shown to selectively impair the regulation of the nuclear transcription factor NF-κB which controls innate immune responses in mammalian cells (Kravchenko et al., 2008). C12-AHL also impaired human dendritic cell functions required for priming of T-cells (Bernatowicz et al., submitted). Since the response to AHL-compounds in mammalian systems is complicated due to the interferences with the adaptive immune system, plants provide an ideal model for the detailed interaction studies of basic innate immune responses and developmental processes with N-acylhomoserine lactones as modifying bacterial effector molecules. Interference of pathogenic as well as symbiotic microbes with the innate immune response via their MAMPS is fundamental for microbe-host interactions. In addition, a multitude of microbial effector molecules are modulating or even initiating specific mutualistic activities in host plants. It is hypothesized, that quorum sensing molecules, like the N-acyl-homoserine lactones of Gram-negative bacteria, should be regarded as important players or modulators of host-bacteria interactions. Other known or still structurally unknown quorum sensing compounds may also serve as central functional glue between root-colonizing / endophytic bacteria and their hosts. While the interactions of plants with pure/single effectors were studied in some detail, the interaction network with other elicitors and effectors of plant responses is still largely unexplored. Functional interaction studies of holobiotic plant systems, including the plant host and its associated microbes, may result in a more profound understanding of the complicated social network of basic innate immune responses with specific effector molecules, if quorum sensing compounds of endophytic bacteria are integrated. Plant - microbiome interactions in the light of the holobiontic concept Higher organisms evolved in the omnipresence of microbes, which could be of pathogenic or symbiotic nature. A framework of response patterns evolved which is known as innate immunity. A major part of this response is the recognition of microbial-associated molecular patterns (MAMP) such as chitin or lipochitooligosaccharides, peptidoglycan, lipopolysaccharides or flagellum structures and the initiation of efficient plant defence reactions (Janeway and Medzhitov, 2002; Jones and Dangl, 2006). However, there are many plant-associated endophytic bacteria known, which are living within plants without triggering persistent and apparent defence responses or visibly do not harm the plant. In some cases, even a stimulation of plant growth due to the presence of specific players within the plant microbiome was reported (Turner et al., 2013). It is now generally accepted, that plant performance and activities can only be characterized and understood completely, if the “holobiont”, the plant plus the intimately associated microbiota, is considered (Zilber-Rosenberg et al., 2008). The evolutionary advantage of an integrated holobiontic system is characterized by a much better adaptability and flexibility towards rapidly changing adverse environmental conditions. It is still mostly unknown, which particular plant genetic loci are controlling the interactions with the plant microbiome and which signals are steering this cooperativity. Mutualistic microbes are able to overcome or short-circuit plant defence responses to enable successful colonization of the host (Zamioudis and Pieterse, 2012; Alqueres et al., 2012). Beneficial associations with microbes other than mycorhiza or Rhizobia are also controlled by systemically regulated or autoregulated processes on top of the basic innate immunity response. The induction of systemic immunity responses like ISR (induced systemic resistance) by some beneficial rhizosphere bacteria or the SAR (systemic acquired resistance) response provoked by pathogens are results of multiple response cascades employed by the plant host to respond to microbial and other environmental interactions. However, the entire response network is by far not yet revealed. For example, bacteria-induced plant responses resulting in improved resistance towards pathogens can also be due to the perception of secondary metabolites, like the surfactin lipopeptide, produced by certain biocontrol Bacilli (Garcia-Gutiérrez et al., 2013) or volatile compounds of plant-associated microbes (Yi et al., 2010). The biocontrol activity of microbial inoculants is probably due to multiple effects of their secondary metabolites to achieve direct inhibition of the pathogenic counterpart as well as an increase of systemic resistance of the plant host. Bacterial quorum sensing molecules like N-acyl homoserine lactones modulate plant responses towards contact with bacteria It is hypothesized, that eukaryotic organisms developed ways to sense microbes in addition to the recognition of their MAMPs by their diffusible small molecules. A very ancient and basic feature of unicellular bacteria is their way of environmental sensing and social communication. In many Gram-negative bacteria the synthesis of autoinducers of the N-acyl-homoserine lactone (AHL) type is tightly regulated in response to cell density or the cell “quorum” (Eberl, 1999). These metabolites are released into the cellular environment to sense the quality of the ecological niche in terms of diffusion space and the density and distribution of their own population. This environmental sensing mechanism helps to adapt the regulation of their gene expression to the given conditions in their habitat and thus optimizes the fitness of the population. Therefore, the generally known term “quorum sensing” (QS) was supplemented by the more broadly defined concept of “efficiency sensing” (Hense et al., 2007). Since this optimization of in situ gene expression is of very basic importance, autoinducer QS-molecules are widespread among bacteria and have quite different molecular structures. N-acyl-homoserine lactones (AHL) are common in Gram-negative bacteria, while cyclic peptides as QS-signals are only to be found in Gram-positive bacteria. The detailed structure of the AHL-molecules can vary; the acyl side chain consists of 4 to 14 carbon atoms and may also contain double bonds. The C3-atom can be hydroxylated or oxidized to a carbonyl-carbon; thus, considerable information and quite different physicochemical properties can be present within these different AHL-structures. As is outlined below, also plants have obviously learned during their evolution to respond to these quorum sensing compounds in different specific ways. We speculate, that QS-compounds are early signals indicating that pathogens are in the surroundings to gather themselves for attack or that mutualists are about to interact with roots. The first demonstration of specific responses of a plant to bacterial N-acyl-homoserine lactones was demonstrated for the legume Medicago truncatula (Mathesius et al., 2003). AHLs from symbiotic (Sinorhizobium meliloti) or pathogenic (Pseudomonas aeruginosa) bacteria provoked at concentrations as low as nano- to micromolar significant changes in the accumulation of over 150 proteins. Auxin-responsive and flavonoid synthesis proteins were induced and also a secretion of plant metabolites that mimic quorum sensing compounds were found, which may have the potential to disrupt quorum sensing signalling by associated bacteria. In tomato plants, a specific induction of systemic resistance proteins after inoculation of the roots with C4- and C6-side chain AHL-producing Serratia liquefaciens MG1 was discovered independently (Hartmann et al., 2004; Schuhegger et al., 2006). The fungal leaf pathogen Alternaria alternata was much less effective, when S. liquefaciens MG 1 wild type had been inoculated to roots of tomato plants as compared to the AHL-negative mutant. It could be shown, that salicylic acid was increased as well as SA- and ethylene-dependent defence genes (i.e. PR1a) in MG1-inoculated plants. Furthermore, Serratia plymuthica HRO-C48, producing C4-/C6- and OHC4-/OHC6-homoserine lactones, is able to induce ISR-like systemic protection of bean and tomato plants against the fungal leaf pathogen Botrytis cinnera; this response was greatly reduced with mutants impaired in AHL-production (Liu et al., 2007; Pang et al., 2009). In contrast, Arabidopsis thaliana responds to short (C4- and C6-) N-acyl AHL-compounds in a different manner: C4- and C6- homoserine lactones alter the expression of selected hormonal regulated genes which results in changes of the plant´s hormone content, in particular an increased auxin / cytokinin ratio (von Rad et al., 2008). However, no systemic resistance response was found to be induced in A. thaliana when roots were stimulated with short side-chain AHLs. Ortiz-Castro et al. (2008) found that C10-homoserine lactone elicited developmental changes in the root system in Arabidopsis plants by altering the expression of cell division and differentiation-related genes. Furthermore, Liu et al. (2012) and Jin et al. (2012) demonstrated that the root stimulatory effect of C6- and C8- homoserine lactones in Arabidopsis plants is mediated through the G-protein coupled receptor encoded by AtGPA1. In mung bean, oxoC10-homoserine lactone activates auxin-induced adventitious root formation via H2O2- and NO-dependent cyclic GMP signaling (Bai et al., 2012). On the other hand, N-acyl-AHLs with C12- and C14- side chains induce systemic resistance to the obligate biotrophic fungus Golovinomyces orontii in A. thaliana and to Blumeria graminis f. sp. hordei in barley (Hordeum vulgare) (Schikora et al., 2011). This response is mediated through altered activation of AtMPK6. The mitogen-activated protein kinases AtMPK3 and AtMPK6 were stronger activated by the model elicitor flg22 in the presence of C12- or C14-AHL compounds which resulted in a higher expression of the defence-related transcription factors WRKY26 and WRKY29 as well as the PR1 gene (Schikora et al., 2011). Thus, AHLs with short and medium side lengths induce developmental effects on root architecture, while long side chain AHLs induce systemic resistance in A. thaliana (Schenk et al., 2012). Furthermore, it was shown, that better water soluble short side chain AHL-compounds are actively taken up into plant roots and transported along the roots into the shoot; in contrast, the lipophilic long acyl side chain AHLs are not transported in barley and A. thaliana. (Götz et al., 2007, von Rad et al., 2008, Sieper et al., 2014). However, no uptake was detected in the legume yam bean (Pachyrhizus erosus (L.) Urban) (Götz et al., 2007). The latter finding corroborates the report of Delalande et al. (2008) that legumes like Lotus corniculatus produce lactonases which degrade AHLs and prevents its uptake and transport. In barley, it could further be demonstrated that C8- and C10-AHLs are taken up in a cell energy dependent manner by ABC-transporters into the root and transported via the central cylinder into the shoot (Sieper et al., 2014). Interestingly, several plants have been demonstrated to produce AHL-mimic substances or to develop other activities influencing quorum sensing of plant associated bacteria (Gao et al., 2003; Bauer and Mathesius, 2004). Flavonoids released by legumes increase the expression of N-acyl-homoserine lactone synthesis genes in Rhizobia (Pérez-Montano et al., 2011): Indole acetic acid and cytokinin biosynthesis of Gypsophila was shown to influence QS, type III secretion system and gall formation activity by Pantoea plantarum (Chalupowicz et al., 2009). On the other hand, tobacco plants have been engineered to produce short- and long-side chain AHL-compounds which could be detected in substantial amounts at leaf and root surfaces as well as in soil (Scott et al., 2006). Constitutive expression of quorum sensing genes in transgenic tobacco plants leads to alteration in induced systemic resistance elicited by the rhizobacterium Serratia marcescens 90-166 (Ryu et al., 2013). Furthermore, transgenic tomato plants engineered to produce different AHL-compounds were demonstrated to alter the activity of plant growth promoting rhizobacteria and resulted e.g. in increased salt tolerance (Barriuso et al., 2008). We hypothesize, that quorum sensing in a plant-microbe holobiont system should be regarded in a bidirectional way with influences from the plant and the microbial partners. Uptake of AHL-compounds and specific perception of AHLs in animal cells were also studied intensively in recent years (Teplitski et al., 2011; Hartmann and Schikora, 2012). 3-oxo-C12-homoserine lactone (C12-AHL), the major AHL-compound of Pseudomonas aeruginosa, was shown to selectively impair the regulation of the nuclear transcription factor NF-κB which controls innate immune responses in mammalian cells (Kravchenko et al., 2008). C12-AHL also impaired human dendritic cell functions required for priming of T-cells (Bernatowicz et al., submitted). Since the response to AHL-compounds in mammalian systems is complicated due to the interferences with the adaptive immune system, plants provide an ideal model for the detailed interaction studies of basic innate immune responses and developmental processes with N-acylhomoserine lactones as modifying bacterial effector molecules. - See more at: http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00131/full#sthash.vXVExt5S.dpuf AU - Hartmann, A. AU - Rothballer, M. AU - Hense, B.A. AU - Schröder, P. C1 - 30815 C2 - 33891 CY - Lausanne TI - Bacterial quorum sensing compounds are important modulators of microbe-plant interactions. JO - Front. Plant Sci. VL - 5 PB - Frontiers Research Foundation PY - 2014 SN - 1664-462X ER - TY - JOUR AU - Gaupels, F. AU - Ghirardo, A. C1 - 25144 C2 - 31830 TI - The extrafascicular phloem is made for fighting. JO - Front. Plant Sci. VL - 4 PB - Frontiers Media PY - 2013 SN - 1664-462X ER - TY - JOUR AB - In plant cells the free radical nitric oxide (NO) interacts both with anti- as well as prooxidants. This review provides a short survey of the central roles of ascorbate and glutathione-the latter alone or in conjunction with S-nitrosoglutathione reductase-in controlling NO bioavailability. Other major topics include the regulation of antioxidant enzymes by NO and the interplay between NO and reactive oxygen species (ROS). Under stress conditions NO regulates antioxidant enzymes at the level of activity and gene expression, which can cause either enhancement or reduction of the cellular redox status. For instance chronic NO production during salt stress induced the antioxidant system thereby increasing salt tolerance in various plants. In contrast, rapid NO accumulation in response to strong stress stimuli was occasionally linked to inhibition of antioxidant enzymes and a subsequent rise in hydrogen peroxide levels. Moreover, during incompatible Arabidopsis thaliana-Pseudomonas syringae interactions ROS burst and cell death progression were shown to be terminated by S-nitrosylation-triggered inhibition of NADPH oxidases, further highlighting the multiple roles of NO during redox-signaling. In chemical reactions between NO and ROS reactive nitrogen species (RNS) arise with characteristics different from their precursors. Recently, peroxynitrite formed by the reaction of NO with superoxide has attracted much attention. We will describe putative functions of this molecule and other NO derivatives in plant cells. Non-symbiotic hemoglobins (nsHb) were proposed to act in NO degradation. Additionally, like other oxidases nsHb is also capable of catalyzing protein nitration through a nitrite- and hydrogen peroxide-dependent process. The physiological significance of the described findings under abiotic and biotic stress conditions will be discussed with a special emphasis on pathogen-induced programmed cell death (PCD). AU - Groß, F. AU - Durner, J. AU - Gaupels, F. C1 - 28157 C2 - 32972 CY - Lausanne TI - Nitric oxide, antioxidants and prooxidants in plant defence responses. JO - Front. Plant Sci. VL - 4 PB - Frontiers Media PY - 2013 SN - 1664-462X ER - TY - JOUR AB - Nitric oxide (NO) is a reactive free radical with pleiotropic functions that participates in diverse biological processes in plants, such as germination, root development, stomatal closing, abiotic stress, and defense responses. It acts mainly through redox-based modification of cysteine residue(s) of target proteins, called protein S-nitrosylation.In this way NO regulates numerous cellular functions and signaling events in plants. Identification of S-nitrosylated substrates and their exact target cysteine residue(s) is very important to reveal the molecular mechanisms and regulatory roles of S-nitrosylation. In addition to the necessity of protein-protein interaction for trans-nitrosylation and denitrosylation reactions, the cellular redox environment and cysteine thiol micro-environment have been proposed important factors for the specificity of protein S-nitrosylation. Several methods have recently been developed for the proteomic identification of target proteins. However, the specificity of NO-based cysteine modification is still less defined. In this review, we discuss formation and specificity of S-nitrosylation. Special focus will be on potential S-nitrosylation motifs, site-specific proteomic analyses, computational predictions using different algorithms, and on structural analysis of cysteine S-nitrosylation. AU - Kovacs, I. AU - Lindermayr, C. C1 - 28258 C2 - 33036 TI - Nitric oxide-based protein modification: Formation and site-specificity of protein S-nitrosylation. JO - Front. Plant Sci. VL - 4 PB - Frontiers Res. PY - 2013 SN - 1664-462X ER - TY - JOUR AB - Nitric oxide (NO) plays an important role in many different physiological processes in plants. It mainly acts by post-translationally modifying proteins. Modification of cysteine residues termed as S-nitrosylation is believed to be the most important mechanism for transduction of bioactivity of NO. The first proteins found to be nitrosylated were mainly of cytoplasmic origin or isolated from mitochondria and peroxisomes. Interestingly, it was shown that redox-sensitive transcription factors are also nitrosylated and that NO influences the redox-dependent nuclear transport of some proteins. This implies that NO plays a role in regulating transcription and/or general nuclear metabolism which is a fascinating new aspect of NO signaling in plants. In this review, we will discuss the impact of S-nitrosylation on nuclear plant proteins with a focus on transcriptional regulation, describe the function of this modification and draw also comparisons to the animal system in which S-nitrosylation of nuclear proteins is a well characterized concept. AU - Mengel, A. AU - Chaki, M. AU - Shekariesfahlan, A. AU - Lindermayr, C. C1 - 28259 C2 - 33037 CY - Lausanne TI - Effect of nitric oxide on gene transcription - S-nitrosylation of nuclear proteins. JO - Front. Plant Sci. VL - 4 PB - Front. Res. PY - 2013 SN - 1664-462X ER - TY - JOUR AB - The formation of 5-aminolevulinic acid (ALA) in tetrapyrrole biosynthesis is widely controlled by environmental and metabolic feedback cues that determine the influx into the entire metabolic path. Because of its central role as the rate-limiting step, we hypothesized a potential role of ALA biosynthesis in tetrapyrrole-mediated retrograde signaling and exploited the direct impact of ALA biosynthesis on nuclear gene expression (NGE) by using two different approaches. Firstly, the Arabidopsisgun1, hy1 (gun2), hy2 (gun3), gun4 mutants showing uncoupled NGE from the physiological state of chloroplasts were thoroughly examined for regulatory modifications of ALA synthesis and transcriptional control in the nucleus. We found that reduced ALA-synthesizing capacity is common to analyzed gun mutants. Inhibition of ALA synthesis by gabaculine (GAB) that inactivates glutamate-1-semialdehyde aminotransferase and ALA feeding of wild-type and mutant seedlings corroborate the expression data of gun mutants. Transcript level of photosynthetic marker genes were enhanced in norflurazon (NF)-treated seedlings upon additional GAB treatment, while enhanced ALA amounts diminish these RNA levels in NF-treated wild-type in comparison to the solely NF-treated seedlings. Secondly, the impact of posttranslationally down-regulated ALA synthesis on NGE was investigated by global transcriptome analysis of GAB-treated Arabidopsis seedlings and the gun4-1 mutant, which is also characterized by reduced ALA formation. A common set of significantly modulated genes was identified indicating ALA synthesis as a potential signal emitter. The over-represented gene ontology categories of genes with decreased or increased transcript abundance highlight a few biological processes and cellular functions, which are remarkably affected in response to plastid-localized ALA biosynthesis. These results support the hypothesis that ALA biosynthesis correlates with retrograde signaling-mediated control of NGE. AU - Czarnecki, O.* AU - Gläßer, C. AU - Chen, J.G.* AU - Mayer, K.F.X. AU - Grimm, B.* C1 - 11310 C2 - 30605 TI - Evidence for a contribution of ALA synthesis to plastid-to-nucleus signaling. JO - Front. Plant Sci. VL - 3 PB - Frontiers Media PY - 2012 SN - 1664-462X ER - TY - JOUR AB - In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future. AU - Leroy, P.* AU - Guilhot, N.* AU - Sakai, H.* AU - Bernard, A.* AU - Choulet, F.* AU - Theil, S.* AU - Reboux, S.* AU - Amano, N.* AU - Flutre, T.* AU - Pelegrin, C.* AU - Ohyanagi, H.* AU - Seidel, M. AU - Giacomoni, F.* AU - Reichstadt, M.* AU - Alaux, M.* AU - Gicquello, E.* AU - Legeai, F.* AU - Cerutti, L.* AU - Numa, H.* AU - Tanaka, T.* AU - Mayer, K.F.X. AU - Itoh, T.* AU - Quesneville, H.* AU - Feuillet, C.* C1 - 10523 C2 - 30308 TI - TriAnnot: A versatile and high performance pipeline for the automated annotation of plant genomes. JO - Front. Plant Sci. VL - 3 IS - JAN PB - Frontiers Research Foundation PY - 2012 SN - 1664-462X ER -