Plant and Cell Physiology (Plant Cell Physiol)

Publications in this journal

• Article: Thermotolerance Responses in Ripening Berries of Vitis vinifera L. cv Muscat Hamburg.

  Pablo Carbonell-Bejerano, Eva Santa María, Rafael Torres-Pérez, Carolina Royo, Diego Lijavetzky, Gema Bravo, Jone Aguirreolea, Manuel Sánchez-Díaz, M Carmen Antolín, José M Martínez-Zapater
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  ABSTRACT: Berry organoleptic properties are highly influenced by ripening environmental conditions. In this study, we used grapevine fruiting cuttings to follow berry ripening under different controlled conditions of temperature and irradiation intensity. Berries ripened at higher temperatures showed reduced anthocyanin accumulation and hastened ripening leading to characteristic malic acid and total acidity drop. The GrapeGen GeneChip® combined with a newly developed GrapeGen 12Xv1 MapMan version were utilised for the functional analysis of berry transcriptomic differences after two weeks treatments from veraison onset. These analyses revealed the establishment of a thermotolerance response in berries under high temperatures marked by the induction of HSP chaperones and the repression of transmembrane transporter encoding transcripts. The thermotolerance response was coincident with up-regulation of ERF subfamily transcription factors and increased ABA levels suggesting their participation in the maintenance of the acclimation response. Lower expression of amino acid transporter encoding transcripts at high temperature correlated with balanced amino acid content suggesting a transcriptional compensation of temperature effects on protein and membrane stability to allow for completion of berry ripening. By contrast, the lower anthocyanins accumulation and higher malate metabolization measured under high temperature might partly result from imbalance in the expression and function of their specific transmembrane transporters and expression changes in genes involved in their metabolic pathways. These results open new views to improve our understanding of berry ripening under high temperatures.
  Plant and Cell Physiology 05/2013;
• Article: The Arabidopsis DUF231 Domain-Containing Protein ESK1 Mediates 2-O- and 3-O-Acetylation of Xylosyl Residues in Xylan.

  Youxi Yuan, Quincy Teng, Ruiqin Zhong, Zheng-Hua Ye
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  ABSTRACT: Xylan, a major polysaccharide in plant lignocellulosic biomass, is acetylated at O-2 and/or O-3 and its acetylation impedes the use of biomass for biofuel production. Currently, it is not known what genes encode acetyltransferases that are responsible for xylan O-acetylation. In this report, we demonstrate an essential role of the Arabidopsis gene ESKIMO1 (ESK1) in xylan O-acetylation during secondary wall biosynthesis. ESK1 expression was found to be regulated by the secondary wall master regulator SND1 and specifically associated with secondary wall biosynthesis. Its encoded protein was localized in the Golgi, the site of xylan biosynthesis. The esk1 mutation caused reductions in secondary wall thickening and stem mechanical strength. Chemical analyses of cell walls revealed that although the esk1 mutation did not cause apparent alterations in the xylan chain length and the abundance of the reducing end sequence, it resulted in a significant reduction in the degree of xylan acetylation. The reduced acetylation of esk1 xylan rendered it to be more accessible and digestible by endoxylanase, leading to generation of shorter xylooligomers compared with the wild type. Further structural analysis of xylan showed that the esk1 mutation caused a specific reduction in 2-O- and 3-O-monoacetylation of xylosyl residues but not in 2,3-di-O-acetylation or 3-O-acetylation of xylosyl residues substituted at O-2 with glucuronic acid. Consistent with ESK1's involvement in xylan O-acetylation, activity assay revealed that the esk1 mutation led to a significant decrease in xylan acetyltransferase activity. Together, these results demonstrate that ESK1 is a putative xylan acetyltransferase required for 2-O- and 3-O-monoacetylation of xylosyl residues and indicate the complexity of the biochemical mechanism underlying xylan O-acetylation.
  Plant and Cell Physiology 05/2013;
• Article: Disruption of the ndhF1 Gene Affects Chlorophyll Fluorescence through State Transition in the Cyanobacterium Synechocystis sp. PCC 6803, resulting in the apparent high efficiency of photosynthesis.

  Takako Ogawa, Tetsuyuki Harada, Hiroshi Ozaki, Kintake Sonoike
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  ABSTRACT: In Synechocystis sp. PCC 6803, the disruption of the ndhF1 gene (slr0844), which encodes a subunit of one of the NDH-1 complexes (NDH-1L complex) serving for respiratory electron transfer, causes the largest change in chlorophyll fluorescence induction kinetics among the kinetics of 750 disruptants searched in the Fluorome, the cyanobacterial chlorophyll fluorescence database. The cause of the explicit phenotype of the ndhF1 disruptant was examined by the measurements of photosynthetic rate, chlorophyll fluorescence and state transition. The results demonstrate that the defects in the respiratory electron transfer have obviously great impact on chlorophyll fluorescence in cyanobacteria. The inactivation of NDH-1L complexes involving electron transfer from NDH-1 to plastoquinone would result in the oxidation of PQ pool, leading to the transition to State 1, where the yield of chlorophyll fluorescence is high. Apparently, respiration, though its rate is far lower than that of photosynthesis, could affect chlorophyll fluorescence through the state transition as leverage. The disruption of the ndhF1 gene caused lower oxygen evolving activity but the estimated electron transport rate from chlorophyll fluorescence measurements was faster in the mutant than in the wild type cells. The discrepancy could be ascribed to the decreased level of non-photochemical quenching due to state transition. One must be cautious to use chlorophyll fluorescence parameter to estimate photosynthesis in mutants defective in state transition.
  Plant and Cell Physiology 05/2013;
• Article: Phytochemical Genomics on the Way.

  Toshiya Muranaka, Kazuki Saito
  Plant and Cell Physiology 05/2013; 54(5):645-646.
• Article: Magnesium Deficiency Phenotypes Upon Multiple Knockout Of Arabidopsis thaliana MRS2 Clade B Genes Can Be Ameliorated By Concomitantly Reduced Calcium Supply.

  Henning Lenz, Vitalij Dombinov, Julia Dreistein, Martin Reinhard, Michael Gebert, Volker Knoop
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  ABSTRACT: Plant MRS2 membrane protein family members have been shown to play important roles in magnesium uptake and homeostasis. Single and double knockouts for two Arabidopsis thaliana genes, AtMRS2-1 and AtMRS2-5, have previously not shown significant phenotypes even under limiting Mg(2+) supply although both are strongly expressed already in early seedlings. Together with AtMRS2-10, these genes form clade B of the AtMRS2 gene family. We now succeeded to obtain homozygous AtMRS2-1/10 double and AtMRS2-1/5/10 triple KO lines after selection under increased magnesium supply. Although wilting early, both new mutant lines develop fully and are fertile also under standard magnesium supply, but show severe developmental retardation under limiting Mg(2+) concentrations. To investigate nutrient dependency of germination and seedling development under various conditions, including variable supplies of Mg(2+), Ca(2+), Zn(2+), Mn(2+), Co(2+), Cd(2+) and Cu(2+), in a reproducible and economical way, we employed a small-scale liquid culturing system in 24-well plate setups. This allowed growing and monitoring individual plantlets of different mutant lines under several nutritional conditions in parallel and the scoring and statistical evaluation of developmental stages and biomass accumulation. Detrimental effects in higher concentrations of these elements were similar in mutants and wild-type. However, growth retardation phenotypes seen upon hydroponic cultivation under low Mg(2+) could be ameliorated when Ca(2+) concentrations were concomitantly lowered, supporting indications for an important interplay of these two most abundant divalent cations in the nutrient homeostasis of plants.
  Plant and Cell Physiology 04/2013;
• Article: Alpha-Tubulin Is Rapidly Phosphorylated in Response to Hyperosmotic Stress in Rice and Arabidopsis.

  Yoshinori Ban, Yuhko Kobayashi, Tomomi Hara, Takahiro Hamada, Takashi Hashimoto, Shin Takeda, Tsukaho Hattori
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  ABSTRACT: By using high-resolution two-dimensional PAGE followed by phosphoprotein-specific staining and peptide mass fingerprint analysis along with other assays, we found that α-tubulin is phosphorylated in response to hyperosmotic stress in rice and Arabidopsis. The onset of the phosphorylation response was as early as 2 min after hyperosmotic stress treatment, and a major proportion of α-tubulin was phosphorylated after 60 min in root tissues. However, the phosphorylated form of α-tubulin was readily dephosphorylated upon stress removal. The phosphorylation site was identified as Thr-349 by comprehensive mutagenesis of Ser/Thr residues in a rice α-tubulin isoform followed by evaluation in cultured cell protoplasts. This residue is located at the surface for the interaction with β-tubulin in polymerized α-β tubulin dimers and has been proposed to be directly involved in this interaction. Thus, α-tubulin phosphorylation was considered to occur on free tubulin dimers in response to hyperosmotic stress. The incorporation of GFP-α-tubulin into cortical microtubules was completely inhibited in transgenic Arabidopsis when Thr-349 was substituted with Glu or Asp. Using transgenic Arabidopsis plants expressing GFP-α-tubulin, we found that hyperosmotic stress causes extensive cortical microtubule depolymerization. Microtubule destabilizing treatments such as propyzamide or oryzalin and temperature stresses resulted in α-tubulin phosphorylation, whereas hyperosmotic stress-induced α-tubulin phosphorylation was partially inhibited by taxol, which stabilizes microtubules. These results and the three-dimensional location of the phosphorylation site suggested that microtubules are depolymerized in response to hyperosmotic stress via α-tubulin phosphorylation. Together, the present study reveals a novel mechanism that globally regulates the microtubule polymerization.
  Plant and Cell Physiology 04/2013;
• Article: Gymnosperms Have Increased Capacity for Electron Leakage to Oxygen (Mehler and PTOX reactions) in Photosynthesis Compared with Angiosperms.

  Masayoshi Shirao, Shu Kuroki, Kaoru Kaneko, Yuriko Kinjo, Michito Tsuyama, Britta Förster, Shunichi Takahashi, Murray R Badger
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  ABSTRACT: Oxygen plays an important role in photosynthesis by participating in a number of O2 consuming reactions. O2 inhibits CO2 fixation by stimulating photorespiration, thus reducing plant production. O2 interacts with photosynthetic electron transport in the chloroplasts' thylakoids in two main ways: by accepting electrons from PSI (Mehler reaction); and by accepting electrons from reduced plastoquinone (PQ) mediated by the plastid terminal oxidase (PTOX). In this study we show using 101 plant species that there is a difference in the potential for photosynthetic electron flow to O2 between angiosperms and gymnosperms. We found, from measurements of Chl fluorescence and leaf absorbance at 830 nm, (i) that electron outflow from PSII, as determined by decay kinetics of Chl fluorescence after application of saturating light pulse, is more rapid in gymnosperms than in angiosperms; (ii) that the reaction center Chl of PSI (P700) is rapidly and highly oxidized in gymnosperms during induction of photosynthesis; (iii) that these differences are dependent on oxygen. Finally, rates of O2 uptake measured by mass spectrometry in the absence of photorespiration were significantly promoted by illumination in dark-adapted leaves of gymnosperms, but not in those of angiosperms. The light-stimulated O2 uptake was around 10% of the maximum O2 evolution in gymnosperms and 1% in angiosperms. These results suggest that gymnosperms have increased capacity for electron leakage to oxygen in photosynthesis compared with angiosperms. The involvement of the Mehler reaction and PTOX in the electron flow to O2 is discussed.
  Plant and Cell Physiology 04/2013;
• Article: Transcriptome Analysis of Japanese Pear (Pyrus pyrifolia Nakai.) Flower Buds Transitioning Through Endodormancy.

  Songling Bai, Takanori Saito, Daisuke Sakamoto, Hiroshi Fujii, Takaya Moriguchi
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  ABSTRACT: The transcriptomes of endodormant and ecodormant Japanese pear (Pyrus pyrifolia Nakai 'Kosui') flower buds were analyzed using RNA-seq technology and compared. Among de novo assembly of 114,191 unigenes, 76,995 unigenes were successfully annotated by BLAST searches against various databases. Gene Ontology (GO) enrichment analysis revealed that oxidoreductases were enriched in the molecular function category, a result consistent with previous observations of notable changes in hydrogen peroxide concentration during endodormancy release. In the GO categories related to biological process, the abundance of DNA methylation-related gene transcripts also significantly changed during endodormancy release, indicating the involvement of epigenetic regulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis also showed the changes in transcript abundance of genes involved in the metabolism of various phytohormones. Genes for both ABA and GA biosynthesis were down-regulated whereas the genes encoding their degradation enzymes were up-regulated during endodormancy release, respectively. In the ethylene pathway, ACC synthase (ACS), a gene encoding the rate-limiting enzyme for ethylene biosynthesis was induced towards endodormancy release. All of these results indicated the involvement of phytohormones in endodormancy release. Furthermore, the expression of dormancy-associated MADS-box (DAM) genes was down-regulated concomitant with endodormancy release, although changes in the abundance of these gene transcripts were not as significant as those identified by transcriptome analysis. Consequently, characterization of the Japanese pear transcriptome during the transition from endormancy to ecodormancy will provide researchers with useful information for data mining and will facilitate further experiments on endodormancy especially in rosaceae fruit trees.
  Plant and Cell Physiology 04/2013;
• Article: In planta Analysis of a cis-Regulatory Cytokinin Response Motif in Arabidopsis and Identification of a Novel Enhancer Sequence.

  Eswarayya Ramireddy, Wolfram G Brenner, Andreas Pfeifer, Alexander Heyl, Thomas Schmülling
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  ABSTRACT: The phytohormone cytokinin plays a key role in regulating plant growth and development and is involved in numerous physiological responses to environmental changes. The type-B response regulators, which regulate the transcription of cytokinin response genes, are a part of the cytokinin signaling system. Arabidopsis thaliana encodes 11 type-B response regulators (type-B ARRs), and some of them were shown to bind in vitro to the core cytokinin response motif (CRM) 5'-(A/G)GAT(T/C)-3' or, in case of ARR1, to an extended motif (ECRM), 5'-AAGAT(T/C)TT-3'. Here we obtained in planta proof for the functionality of the latter motif. Promoter deletion analysis of the primary cytokinin response gene ARR6 showed that a combination of two extended motifs within the promoter is required for mediating the full transcriptional activation by ARR1 and other type-B ARRs. CRMs were found to be overrepresented in the vicinity of ECRMs in the promoters of cytokinin-regulated genes suggesting their functional relevance. Moreover, an evolutionary conserved 27 bp-long region between -220 and -193 bp was identified and shown to be required for the full activation by type-B ARRs and the response to cytokinin. This novel enhancer is not bound by the DNA binding domain of ARR1, indicating that additional proteins might be involved in mediating the transcriptional cytokinin response. Furthermore, genome-wide expression profiling identified genes, among them ARR16, whose induction by cytokinin depends on both ARR1 and specific other type-B ARRs. This together with the ECRM/CRM sequence clustering indicates cooperative action of different type-B ARRs for the activation of particular target genes.
  Plant and Cell Physiology 04/2013;
• Article: Low-pH and Aluminium Resistance in Arabidopsis Correlates with High Cytosolic Magnesium Content and Increased Magnesium Uptake by Plant Roots.

  Jayakumar Bose, Olga Babourina, Sergey Shabala, Zed Rengel
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  ABSTRACT: Low-pH stress and Al(3+) toxicity affect root growth in acid soils. It was hypothesised that capacity of genotypes to maintain Mg(2+) uptake in acidic environments may contribute to low-pH and Al resistance, but explicit evidence is lacking. In this work, Al-resistant alr104 mutant and two Al-sensitive mutants (als5 and als3) of Arabidopsis thaliana were compared with the wild type (Col-0) for Mg(2+) uptake and intracellular Mg(2+) concentration under low-pH and combined low-pH/Al stresses. Magnesium accumulation in roots was measured in long-term (7 days) experiments. The Mg(2+) fluxes were measured using ion-sensitive microelectrodes at the distal elongation and the mature root zones in short-term (0-60 min) experiments. Intracellular Mg(2+) concentrations were measured in intact root cells at the distal elongation zone using magnesium-specific fluorescent dye and fluorescent lifetime imaging (FLIM) analysis. Under low-pH stress, Arabidopsis mutants als5 and alr104 maintained higher Mg concentration in roots, and had greater Mg(2+) influx than the wild type and als3 mutant. Under combined low-pH/Al treatment, Al-resistant genotypes (wild type and alr104) maintained higher Mg(2+) accumulation, had higher Mg2+ influx and higher intracellular Mg(2+) concentration than Al-sensitive genotypes (als3 and als5). Overall, these results show that increased Mg(2+) uptake correlates with enhanced capacity of Arabidopsis genotypes to cope with low-pH and combined low-pH/Al stresses.
  Plant and Cell Physiology 04/2013;
• Article: "The Plant S1-Like Nuclease Family Has Evolved A Highly Diverse Range Of Catalytic Capabilities"

  Krzysztof Lesniewicz, Wojciech M Karlowski, Joanna R Pienkowska, Piotr Krzywkowski, Elzbieta Poreba
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  ABSTRACT: Plant S1-like nucleases, often referred to as nuclease I enzymes, are the main class of enzymes involved in nucleic acid degradation during plant programmed cell death. The catalytically active site of these enzymes shows a significant similarity to the well-described P1 nuclease from Penicillium citrinum. Previously published studies reported that plant S1-like nucleases possess catalytic activities similar to their fungal orthologs, i.e. it hydrolyses the ssDNA and RNA and less efficiently dsDNA in the presence of zinc ions. In this paper, we describe a comprehensive study of the nucleolytic activities of all Arabidopsis S1-like paralogs. Our results revealed that different members of this family are characterized by a surprisingly large variety of catalytic properties. We found that, in addition to Zn(2+)-dependent enzymes, this family also comprises nucleases activated by Ca(2+) and Mn(2+), which implies that the apparently well-known S1 nuclease active site in plant nucleases is able to cooperate with different activatory ions. Moreover, particular members of this class differ in their optimum pH value and substrate specificity. These results shed new light on the widely accepted classification of plant nucleases which is based on the assumption that the catalytic requirements of plant nucleases reflect their phylogenetic origin. Our results imply the need to redefine the understanding of the term "nuclease I". Analysis of the phylogenetic relationships between S1-like enzymes shows that plant representatives of this family evolve toward an increase in catalytic diversity. The importance of this process for the biological functions of plant S1-type enzymes is discussed.
  Plant and Cell Physiology 04/2013;
• Article: AtHO1 is involved in iron homeostasis in a NO-dependent manner.

  Hua Li, Jian Bo Song, Wen Ting Zhao, Zhi Min Yang
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  ABSTRACT: AtHO1 (HY1) encodes heme oxygenase-1 in Arabidopsis, catalyzing cleavage of heme to biliverdin with the release of iron and carbon monoxide (CO). Our previous study show that CO as an endogenous component is able to improve plant adaptation to iron deficiency. Here, we performed a genetic study to identify further the putative role of AtHO1 in iron deficient response. Iron deficiency induced AtHO1 expression at transcriptional and translational levels. Evidence has been provided that over-expression of AtHO1 could confer plant tolerance to iron deficiency by improving expression of AtFIT, AtFRO2, AtIRT1, activity of ferric-chelate reductase (FCR), and iron accumulation. In contrast, RNA-interference of AtHO1 expression in 35S::AntiHO1 plants and AtHO1 loss of function (hy1 mutant) resulted in adverse phenotypes. In 35S::AtHO1 transgenic lines, a higher level of CO and water-soluble iron and a lower level of heme were identified, suggesting that AtHO1-regulated iron homeostasis was possibly through the catabolism of heme to produce CO and free iron. Because nitric oxide (NO) is known to regulate iron homeostasis in plants, the connection between AtHO1 expression and NO action was examined. AtHO1 over-expressing plants generated more NO, whereas knock-down of AtHO1 expression reduced the level of NO in plants. The NO scavenger cPTIO caused a decrease of AtHO1-induced FCR activity. Under both iron sufficient and deficient conditions, administration of the NO donor SNP induced FCR activity in the hy1 plants. These results suggest that AtHO1 is involved in iron homeostasis in a NO-dependent manner.
  Plant and Cell Physiology 04/2013;
• Article: Stress Enhances the Synthesis of Secondary Plant Products: the Impact of the Stress-Related Over-Reduction on the Accumulation of Natural Products.

  Dirk Selmar, Maik Kleinwächter
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  ABSTRACT: Spice and medicinal plants grown under water deficiency conditions reveal much higher concentrations of relevant natural products compared to identical plants of the same species cultivated with an ample water supply. For the first time, experimental data related to this well-known phenomenon has been collected and a putative mechanistic concept considering general plant physiological and biochemical aspects is presented. Water shortage induces drought stress-related metabolic responses and, due to stomatal closure, the uptake of CO2 decreases significantly. As a result, the consumption of reduction equivalents (NADPH+H(+)) for CO2-fixation via the Calvin cycle declines considerably, generating a large oxidative stress and an oversupply of reduction equivalents. As a consequence, metabolic processes are shifted towards biosynthetic activities that consume reduction equivalents. Accordingly, the synthesis of reduced compounds, such as isoprenoids, phenols or alkaloids, is enhanced.
  Plant and Cell Physiology 04/2013;
• Article: Differential expression of three BOR1 genes corresponding to different genomes in response to boron conditions in hexaploid Wheat (Triticum aestivum L.).

  Sumana Leaungthitikanchana, Takahiro Fujibe, Mayuki Tanaka, Sheliang Wang, Naoyuki Sotta, Junpei Takano, Toru Fujiwara
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  ABSTRACT: Boron (B) is an essential micronutrient for plants. Efflux-type B transporters, BORs, have been identified in Arabidopsis thaliana and rice (Takano et al., 2002; Nakagawa et al., 2007). Here we identified BOR1 genes encoding B efflux transporters, from the hexaploid genome of wheat (Triticum aestivum L.). We cloned three genes closely related to Os BOR1 and named as Ta BOR1.1, Ta BOR1.2 and Ta BOR1.3. All three Ta BOR1s showed B efflux activities when expressed in tobacco BY-2 cells. Ta BOR1s-green fluorescent protein (GFP) fusion proteins were expressed in Arabidopsis leaf cells localized in the plasma membrane. Transcript accumulation patterns of three genes differ in terms of tissue specificity and B nutrition responses. In roots, transcripts for all three genes accumulated abundantly while in shoots, Ta BOR1.2 transcript is the most abundant followed by those of Ta BOR1.1 and Ta BOR1.3. Accumulation of Ta BOR1.1 transcript is up-regulated under B deficiency conditions in both roots and shoots. In contrast, Ta BOR1.2 transcript accumulation significantly increased in roots under the excess B condition. Ta BOR1.3 transcript accumulation was reduced under the excess B condition. Taken together, these results demonstrated that Ta BOR1s are the B efflux transporters in wheat and interestingly the genes on the A, B, and D genomes have different expression patterns.
  Plant and Cell Physiology 04/2013;
• Article: Analysis of Alfalfa Root Transcriptome in Response to Salinity Stress.

  Olga A Postnikova, Jonathan Shao, Lev G Nemchinov
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  ABSTRACT: Salinity is one of the major abiotic factors affecting alfalfa productivity. Identifying genes that control this complex trait will provide critical insights for alfalfa breeding programs. At the moment, no studies have been published on a deep sequencing-based profiling of the alfalfa transcriptome in response to salinity stress. Observations gathered through research on reference genomes may not always be applicable to alfalfa. In this work, Illumina RNA-sequencing was performed in two alfalfa genotypes contrasting in salt tolerance, in order to estimate a broad spectrum of genes affected by salt stress. A total of 367, 619, 586 short reads were generated from cDNA libraries originated from roots of both lines. More than 60,000 Tentative Consensus sequences (TCs) were obtained and among them 74.5% had a significant similarity with proteins in the NCBI database. Mining of simple sequence repeats from all TCs revealed 6,496 SSR belonging to 3,183 annotated unigenes. Bioinformatics analysis showed that the expression of 1165 genes, including 86 transcription factors (TFs) was significantly altered under salt stress. About 40% of differentially expressed genes were assigned to known GO categories using Arabidopsis gene ontology. A random check of differentially expressed genes by quantitative real-time PCR confirmed the bioinformatic analysis of the RNA-seq data. A number of salt-responsive genes in both tested genotypes were identified and assigned to functional classes, and gene-candidates with roles in the adaptation to salinity were proposed. Alfalfa-specific data on salt-responsive genes obtained in this work will be useful in understanding the molecular mechanisms of salinity tolerance in alfalfa.
  Plant and Cell Physiology 04/2013;
• Article: Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals.

  Jordan A Ramilowski, Satoru Sawai, Hikaru Seki, Keiichi Mochida, Takuhiro Yoshida, Tetsuya Sakurai, Toshiya Muranaka, Kazuki Saito, Carsten O Daub
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  ABSTRACT: Medicinal and industrial properties of phytochemicals (eq., glycyrrhizin) from the root of Glycyrrhiza uralensis (licorice plant) made it an attractive, multimillion-dollar trade item. Bioengineering of plants is one of the solutions to answer such high market demand and to prevent plants from the extinction. Unfortunately limited genomic information on medicinal plants restricts their research and thus biosynthetic mechanisms of many important phytochemicals are still poorly understood. In this work we leveraged the power of de-novo (no reference genome sequence available) assembly of Illumina RNA-seq data to study the transcriptome of the licorice plant. Our analysis is based on sequencing results of libraries made from samples that belonged to different tissues (root an leaf) and were collected at different seasons and from two slightly distinct strains (glycyrrhizin low and high producing strain). We provide functional annotations and the expression profile of 43,882 assembled unigenes, which are suitable for various further studies. Here, we searched for Glycyrrhiza uralensis specific enzymes involved in isoflavonoid biosynthesis as well as elucidated putative cytochrome P450 (CYP) enzymes and putative vacuolar saponin transporters involved in glycyrrhizin production in the licorice root. To disseminate the data and the analysis results we constructed publicly available the Glycyrrhiza uralensis database. This work will contribute to a better understanding of the secondary metabolites biosynthetic pathways in licorice plants, and possibly in other medicinal plants, and will provide an important resource to further advance transcriptomics studies in legumes.
  Plant and Cell Physiology 04/2013;
• Article: Transcriptome analysis of WIPK/SIPK-suppressed plants reveals induction by wounding of disease resistance-related genes prior to the accumulation of salicylic acid.

  Shinpei Katou, Nobuhide Asakura, Tomoya Kojima, Ichiro Mitsuhara, Shigemi Seo
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  ABSTRACT: Salicylic acid (SA) plays a key role in plant resistance to pathogens. Accumulation of SA is induced by wounding in tobacco plants in which the expression of WIPK and SIPK, two mitogen-activated protein kinases, is suppressed. Here, the mechanisms underlying the abnormal accumulation of SA in WIPK/SIPK-suppressed plants have been characterized. SA accumulation started around 12 h after wounding and was inhibited by cycloheximide (CHX), a protein synthesis inhibitor. SA accumulation, however, was enhanced several-fold when leaf discs were transferred onto CHX after floating on water for 6 h or more. Temporal and spatial analyses of wound-induced and CHX-enhanced SA accumulation suggested that wounding induces activators for SA accumulation followed by the generation of repressors, and late CHX treatment inhibits the production of repressors more efficiently than that of activators. Microarray analysis revealed that the expression of many disease resistance-related genes including N, a Resistance (R) gene for Tobacco mosaic virus and R gene-like genes was up-regulated in wounded WIPK/SIPK-suppressed plants. Expression of the N gene and R gene-like genes peaked earlier than that of most other genes as well as SA accumulation, and was mainly induced in those parts of leaf discs where SA was highly accumulated. Moreover, wound-induced SA accumulation was decreased by the treatments which compromise function of R proteins. These results indicate that signaling leading to the expression of disease resistance-related genes is activated by wounding in WIPK/SIPK-suppressed plants, and induction of R gene and R gene-like genes might lead to the biosynthesis of SA.
  Plant and Cell Physiology 04/2013;
• Article: Genome stability of Arabidopsis atm, ku80 and rad51b mutants: somatic and transgenerational responses to stress.

  Youli Yao, Andriy Bilichak, Viktor Titov, Andrey Golubov, Igor Kovalchuk
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  ABSTRACT: DNA double-strand breaks (DSBs) can be repaired via two main mechanisms: non-homologous end joining (NHEJ) and homologous recombination (HR). Our previous work showed that exposure to abiotic stresses resulted in an increase in point mutation frequency (PMF) and homologous recombination frequency (HRF), and these changes were heritable. We hypothesized that mutants impaired in DSB recognition and repair would also be deficient in somatic and transgenerational changes in PMF and HRF. To test this hypothesis, we analyzed genome stability of the Arabidopsis (Arabidopsis thaliana) mutants deficient in ATM (communication between DNA strand break recognition and the repair machinery), KU80 (deficient in NHEJ), and RAD51B (deficient in HR repair) genes. We found that all three mutants exhibited higher levels of DSBs. Plants impaired in ATM had lower levels of spontaneous PMF and HRF, whereas ku80 plants had higher ones. Plants impaired in RAD51B had lower HRF. HRF in wild-type, atm and rad51b plants increased in response to several abiotic stressors, whereas it did not increase in ku80 plants. The progeny of stressed wild- type and ku80 plants exhibited an increase in HRF in response to all stresses, and the increase was higher in ku80 plants. The progeny of atm plants showed an increase in HRF only when the parental generation was exposed to cold or flood, whereas the progeny of rad51b plants completely lacked a transgenerational increase in HRF.Our experiments showed that mutants impaired in the recognition and repair of DSBs exhibited changes in the efficiency of DNA repair as reflected by changes in strand breaks, point mutation and homologous recombination frequency. They also showed that the HR RAD51B protein and the protein ATM that recognized damaged DNA might play an important role in transgenerational changes in HRF.
  Plant and Cell Physiology 04/2013;
• Article: SS-mPMG and SS-GA: Tools for Finding Pathways and Dynamic Simulation of Metabolic Networks.

  Tetsuo Katsuragi, Naoaki Ono, Keiichi Yasumoto, Md Altaf-Ul-Amin, Masami Y Hirai, Kansuporn Sriyudthsak, Yuji Sawada, Yui Yamashita, Yukako Chiba, Hitoshi Onouchi, Toru Fujiwara, Satoshi Naito, Fumihide Shiraishi, Shigehiko Kanaya
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  ABSTRACT: Metabolomics analysis tools can provide quantitative information on the concentration of metabolites in an organism. In this paper, we propose the minimum pathway model generator tool for simulating the dynamics of metabolite concentrations (SS-mPMG) and a tool for parameter estimation by genetic algorithm (SS-GA). SS-mPMG can extract a subsystem of the metabolic network from the genome-scale pathway maps to reduce the complexity of the simulation model and automatically construct a dynamic simulator to evaluate the experimentally observed behavior of metabolites. Using this tool, we show that stochastic simulation can reproduce experimentally observed dynamics of amino acid biosynthesis in Arabidopsis thaliana. In this simulation, SS-mPMG extracts the metabolic network subsystem from published databases. The parameters needed for the simulation are determined using a genetic algorithm to fit the simulation results to the experimental data. We expect that SS-mPMG and SS-GA will help researchers to create relevant metabolic networks and carry out simulations of metabolic reactions derived from metabolomics data.
  Plant and Cell Physiology 04/2013;