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A Naturally Associated Rhizobacterium of Arabidopsis thaliana Induces a Starvation-Like Transcriptional Response while Promoting Growth  [PDF]
Jens Schwachtje, Silke Karojet, Ina Thorm?hlen, Carolin Bernholz, Sabine Kunz, Stephan Brouwer, Melanie Schwochow, Karin K?hl, Joost T. van Dongen
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0029382
Abstract: Plant growth promotion by rhizobacteria is a known phenomenon but the underlying mechanisms are poorly understood. We searched for plant growth-promoting rhizobacteria that are naturally associated with Arabidopsis thaliana to investigate the molecular mechanisms that are involved in plant growth-promotion. We isolated a Pseudomonas bacterium (Pseudomonas sp. G62) from roots of field-grown Arabidopsis plants that has not been described previously and analyzed its effect on plant growth, gene expression and the level of sugars and amino acids in the host plant. Inoculation with Pseudomonas sp. G62 promoted plant growth under various growth conditions. Microarray analysis revealed rapid changes in transcript levels of genes annotated to energy-, sugar- and cell wall metabolism in plants 6 h after root inoculation with P. sp. G62. The expression of several of these genes remained stable over weeks, but appeared differentially regulated in roots and shoots. The global gene expression profile observed after inoculation with P. sp. G62 showed a striking resemblance with previously described carbohydrate starvation experiments, although plants were not depleted from soluble sugars, and even showed a slight increase of the sucrose level in roots 5 weeks after inoculation. We suggest that the starvation-like transcriptional phenotype - while steady state sucrose levels are not reduced - is induced by a yet unknown signal from the bacterium that simulates sugar starvation. We discuss the potential effects of the sugar starvation signal on plant growth promotion.
Effects of the Plant Growth-Promoting Bacterium Burkholderia phytofirmans PsJN throughout the Life Cycle of Arabidopsis thaliana  [PDF]
María Josefina Poupin, Tania Timmermann, Andrea Vega, Ana Zu?iga, Bernardo González
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0069435
Abstract: Plant growth-promoting rhizobacteria (PGPR) induce positive effects in plants, such as increased growth or reduced stress susceptibility. The mechanisms behind PGPR/plant interaction are poorly understood, as most studies have described short-term responses on plants and only a few studies have analyzed plant molecular responses under PGPR colonization. Here, we studied the effects of the PGPR bacterial model Burkholderia phytofirmans PsJN on the whole life cycle of Arabidopsis thaliana plants. We reported that at different plant developmental points, strain PsJN can be found in the rhizosphere and also colonizing their internal tissues. In early ontogeny, strain PsJN increased several growth parameters and accelerated growth rate of the plants. Also, an Arabidopsis transcriptome analysis revealed that 408 genes showed differential expression in PsJN-inoculated plants; some of these genes are involved in stress response and hormone pathways. Specifically, genes implicated in auxin and gibberellin pathways were induced. Quantitative transcriptional analyses of selected genes in different developmental stages revealed that the beginning of these changes could be evidenced early in development, especially among the down-regulated genes. The inoculation with heat-killed bacteria provoked a more severe transcriptional response in plants, but was not able to induce plant growth-promotion. Later in ontogeny, the growth rates of inoculated plants decreased with respect to the non-inoculated group and, interestingly, the inoculation accelerated the flowering time and the appearance of senescence signs in plants; these modifications correlate with the early up-regulation of flowering control genes. Then, we show that a single inoculation with a PGPR could affect the whole life cycle of a plant, accelerating its growth rate and shortening its vegetative period, both effects relevant for most crops. Thus, these findings provide novel and interesting aspects of these relevant biological interactions.
Glucosinolates are produced in trichomes of Arabidopsis thaliana  [PDF]
Henning Frerigmann,Christoph B?ttcher,Dunja Baatout,Tamara Gigolashvili
Frontiers in Plant Science , 2012, DOI: 10.3389/fpls.2012.00242
Abstract: Glucosinolates (GS) are important plant secondary metabolites in plant resistance to herbivores, bacteria, and fungi, which have been shown to be accumulating in different organs and tissue types at varying concentrations. There are more than 200 GS species found in order Brassicales and presence of these compounds is well documented on organ-specific but not on cell-specific level. We used UPLC/ESI-QTOF-MS to measure the presence of GS and qRT-PCR to analyse the expression of GS biosynthetic and regulatory genes in isolated Arabidopsis thaliana trichomes. Trichomes of Arabidopsis are shown to synthesize chemoprotective aliphatic glucosinolates (AGS) and indolic glucosinolates (IGS), which are known for their biological activities against fungi, bacterial pathogens, or herbivores. UPLC/ESI-QTOF-MS analysis of various IGS mutants reveal increased or decreased levels of IGS in trichomes of gain- and loss-of-function mutants correspondingly. Using pMYB51/HIG1-uidA and pMYB28/PMG1/HAG1-uidA reporter plants we demonstrate that production of these important compounds is activated in trichomes of leaves or inflorescences in response to wounding. Since trichomes represent the first interface in plant-environment interactions, the possible role of GS containing trichomes in plant defense or signaling is discussed.
Arabidopsis thaliana  [PDF]
Jo Wixon
Comparative and Functional Genomics , 2001, DOI: 10.1002/cfg.75
Abstract: Arabidopsis is universally acknowledged as the model for dicotyledonous crop plants. Furthermore, some of the information gleaned from this small plant can be used to aid work on monocotyledonous crops. Here we provide an overview of the current state of knowledge and resources for the study of this important model plant, with comments on future prospects in the field from Professor Pamela Green and Dr Sean May.
Effects of antibiotics on root of Arabidopsis thaliana  [cached]
Duan Zhikun,Duan Hongying,He Yunlong,Song Jianying
Analele ?tiin?ifice Ale Universit??ii Alexandru Ioan Cuza din Ia?i,Sectiunea II A : Genetica si Biologie Moleculara , 2009,
Abstract: In this article, it was found that growth and development of Arabidopsis thaliana seedling root were evidently affected by kanamycin and Hygromycin. Compared to the controls, main root of Arabidopsis thaliana seedling on MS with kanamycin or Hygromycin was very short, lateral root was not formed. In addition, cells in the meristematic zone of root tip exhibited abnormal array, weak division ability and large intercellular space. Therefore, it is presumed that kanamycin and Hygromycin might influence growth of main root and formation of lateral root of Arabidopsis seedlings by restraining synthesis of some proteins
The Pattern of Polymorphism in Arabidopsis thaliana  [PDF]
Magnus Nordborg,Tina T. Hu,Yoko Ishino,Jinal Jhaveri,Christopher Toomajian,Honggang Zheng,Erica Bakker,Peter Calabrese,Jean Gladstone,Rana Goyal,Mattias Jakobsson,Sung Kim,Yuri Morozov,Badri Padhukasahasram,Vincent Plagnol,Noah A. Rosenberg,Chitiksha Shah,Jeffrey D. Wall,Jue Wang,Keyan Zhao,Theodore Kalbfleisch,Vincent Schulz,Martin Kreitman,Joy Bergelson
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0030196
Abstract: We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics.
The pattern of polymorphism in Arabidopsis thaliana.
Nordborg Magnus,Hu Tina T,Ishino Yoko,Jhaveri Jinal
PLOS Biology , 2005,
Abstract: We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics.
The Pattern of Polymorphism in Arabidopsis thaliana  [PDF]
Magnus Nordborg ,Tina T Hu,Yoko Ishino,Jinal Jhaveri,Christopher Toomajian,Honggang Zheng,Erica Bakker,Peter Calabrese,Jean Gladstone,Rana Goyal,Mattias Jakobsson,Sung Kim,Yuri Morozov,Badri Padhukasahasram,Vincent Plagnol,Noah A Rosenberg,Chitiksha Shah,Jeffrey D Wall,Jue Wang,Keyan Zhao,Theodore Kalbfleisch,Vincent Schulz,Martin Kreitman,Joy Bergelson
PLOS Biology , 2005, DOI: 10.1371/journal.pbio.0030196
Abstract: We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics.
The Alphabet of Galactolipids in Arabidopsis thaliana  [PDF]
Amina Ibrahim,Ivo Feussner
Frontiers in Plant Science , 2011, DOI: 10.3389/fpls.2011.00095
Abstract: Galactolipids constitute the major lipid class in plants. In recent years oxygenated derivatives of galactolipids have been detected. They are discussed as signal molecules during leaf damage, since they accumulate in wounded leaves in high levels. Using different analytical methods such as nuclear magnetic resonance, infra-red spectroscopy, and high performance liquid chromatography/mass spectrometry (HPLC/MS) earlier reports focused on the analysis of either oxidized or non-oxidized species and needed high levels of analytes. Here, we report on the analysis of the galactolipid subfraction of the Arabidopsis leaf lipidome by an improved HPLC/MS2-based method that is fast, robust, and comparatively simple in its performance. Due to a combination of phase partitioning, solid phase fractionation, liquid chromatography, and MS2 experiments this method has high detection sensitivity and requires only low amounts of plant material. With this method 167 galactolipid species were detected in leaves of Arabidopsis thaliana. Out of these 79 being newly described species. From all species the head group and acyl side chains were identified via MS2 experiments. Moreover, the structural identification was supported by HPLC/time-of-flight (TOF)-MS and gas chromatography (GC)/MS analysis. The quantification of different galactolipid species that accumulated 30 min after a mechanical wounding in A. thaliana leaves showed that the oxidized acyl side chains in galactolipids are divided into 65% cyclopentenones, 27% methyl-branched ketols, 3.8% hydroperoxides/straight-chain ketols, 2.0% hydroxides, and 2.6% phytoprostanes. In comparison to the free cyclopentenone derivatives, the esterified forms occur in a 149-fold excess supporting the hypothesis that galactolipids might function as storage compounds for cyclopentenones. Additional analysis of the ratio of non-oxidized to oxidized galactolipid species in leaves of wounded plants was performed resulting in a ratio of 2.0 in case of monogalactosyl diacylglycerol (MGD), 8.1 in digalactosyl diacylglycerol (DGD), and 0.6 in the acylated MGD. This indicates that galactolipid oxidation is a major and rapid metabolic process that occurs class specific.
Biochemical and Structural Properties of Cyanases from Arabidopsis thaliana and Oryza sativa  [PDF]
Dan Qian,Lin Jiang,Lu Lu,Chunhong Wei,Yi Li
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0018300
Abstract: Cyanate is toxic to all organisms. Cyanase converts cyanate to CO2 and NH3 in a bicarbonate-dependent reaction. The biophysical functions and biochemical characteristics of plant cyanases are poorly studied, although it has been investigated in a variety of proteobacteria, cyanobacteria and fungi. In this study, we characterised plant cyanases from Arabidopsis thaliana and Oryza sativa (AtCYN and OsCYN). Prokaryotic-expressed AtCYN and OsCYN both showed cyanase activity in vitro. Temperature had a similar influence on the activity of both cyanases, but pH had a differential impact on AtCYN and OsCYN activity. Homology modelling provided models of monomers of AtCYN and OsCYN, and a coimmunoprecipitation assay and gel filtration indicated that AtCYN and OsCYN formed homodecamers. The analysis of single-residue mutants of AtCYN indicated that the conserved catalytic residues also contributed to the stability of the homodecamer. KCNO treatment inhibited Arabidopsis germination and early seedling growth. Plants containing AtCYN or OsCYN exhibited resistance to KCNO stress, which demonstrated that one role of cyanases in plants is detoxification. Transcription level of AtCYN was higher in the flower than in other organs of Arabidopsis. AtCYN transcription was not significantly affected by KCNO treatment in Arabidopsis, but was induced by salt stress. This research broadens our knowledge on plant detoxification of cyanate via cyanase.
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