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Journal Cover Plant Molecular Biology
  [SJR: 1.915]   [H-I: 137]   [9 followers]  Follow
    
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 1573-5028 - ISSN (Online) 0167-4412
   Published by Springer-Verlag Homepage  [2353 journals]
  • An integrative overview of the molecular and physiological responses of
           sugarcane under drought conditions
    • Authors: Camilo Elber Vital; Andrea Giordano; Eduardo de Almeida Soares; Thomas Christopher Rhys Williams; Rosilene Oliveira Mesquita; Pedro Marcus Pereira Vidigal; Amanda de Santana Lopes; Túlio Gomes Pacheco; Marcelo Rogalski; Humberto Josué de Oliveira Ramos; Marcelo Ehlers Loureiro
      Pages: 577 - 594
      Abstract: Abstract Drought is the main abiotic stress constraining sugarcane production. However, our limited understanding of the molecular mechanisms involved in the drought stress responses of sugarcane impairs the development of new technologies to increase sugarcane drought tolerance. Here, an integrated approach was performed to reveal the molecular and physiological changes in two closely related sugarcane cultivars, including the most extensively planted cultivar in Brazil (cv. RB867515), in response to moderate (−0.5 MPa) and severe (−1 MPa) drought stress at the transcriptional, translational, and posttranslational levels. The results show common and cultivar exclusive changes in specific genes related to photosynthesis, carbohydrate, amino acid, and phytohormone metabolism. The novel phosphoproteomics and redox proteomic analysis revealed the importance of posttranslational regulation mechanisms during sugarcane drought stress. The shift to soluble sugar, secondary metabolite production, and activation of ROS eliminating processes in response to drought tolerance were mechanisms exclusive to cv. RB867515, helping to explain the better performance and higher production of this cultivar under these stress conditions.
      PubDate: 2017-08-01
      DOI: 10.1007/s11103-017-0611-y
      Issue No: Vol. 94, No. 6 (2017)
       
  • Dynamics of tobacco DNA topoisomerases II in cell cycle regulation: to
           manage topological constrains during replication, transcription and
           mitotic chromosome condensation and segregation
    • Authors: Badri Nath Singh; V. Mohan Murali Achary; Varakumar Panditi; Sudhir K. Sopory; Malireddy K. Reddy
      Pages: 595 - 607
      Abstract: Key message The topoisomerase II expression varies as a function of cell proliferation. Maximal topoisomerase II expression was tightly coupled to S phase and G2/M phase via both transcriptional and post-transcriptional regulation. Investigation in meiosis using pollen mother cells also revealed that it is not the major component of meiotic chromosomes, it seems to diffuse out once meiotic chromosomal condensation is completed. Synchronized tobacco BY-2 cell cultures were used to study the role of topoisomerase II in various stages of the cell cycle. Topoisomerase II transcript accumulation was observed during the S- and G2/M- phase of cell cycle. This biphasic expression pattern indicates the active requirement of topoisomerase II during these stages of the cell cycle. Through immuno-localization of topoisomerase II was observed diffusely throughout the nucleoplasm in interphase nuclei, whereas, the nucleolus region exhibited a more prominent immuno-positive staining that correlated with rRNA transcription, as shown by propidium iodide staining and BrUTP incorporation. The immuno-staining analysis also showed that topoisomerase II is the major component of mitotic chromosomes and remain attached to the chromosomes during cell division. The inhibition of topoisomerase II activity using specific inhibitors revealed quite dramatic effect on condensation of chromatin and chromosome individualization from prophase to metaphase transition. Partially condensed chromosomes were not arranged on metaphase plate and chromosomal perturbations were observed when advance to anaphase, suggesting the importance of topoisomerase II activity for proper chromosome condensation and segregation during mitosis. Contrary, topoisomerase II is not the major component of meiotic chromosomes, even though mitosis and meiosis share many processes, including the DNA replication, chromosome condensation and precisely regulated partitioning of chromosomes into daughter cells. Even if topoisomerase II is required for individualization and condensation of meiotic chromosomes, it seems to diffuse out once meiotic chromosomal condensation is completed.
      PubDate: 2017-08-01
      DOI: 10.1007/s11103-017-0626-4
      Issue No: Vol. 94, No. 6 (2017)
       
  • Time-dependent leaf proteome alterations of Brachypodium distachyon in
           response to drought stress
    • Authors: Ozge Tatli; Bahar Sogutmaz Ozdemir; Gizem Dinler Doganay
      Pages: 609 - 623
      Abstract: Key message For the first time, a comprehensive proteome analysis was conducted on Brachypodium leaves under drought stress. Gradual changes in response to drought stress were monitored. Drought is one of the major stress factors that dramatically affect the agricultural productivity worldwide. Improving the yield under drought is an urgent challenge in agriculture. Brachypodium distachyon is a model species for monocot plants such as wheat, barley and several potential biofuel grasses. In the current study, a comprehensive proteome analysis was conducted on Brachypodium leaves under different levels of drought application. To screen gradual changes upon drought, Brachypodium leaves subjected to drought for 4, 8 and 12 days were collected for each treatment day and relative water content of the leaves was measured for each time point. Cellular responses of Brachypodium were investigated through a proteomic approach involving two dimensional difference gel electrophoresis (2D-DIGE) and mass spectrometry (MS). Among 497 distinct spots in Brachypodium protein repertoire, a total of 13 differentially expressed proteins (DEPs) were identified as responsive to drought by mass spectrometry and classified according to their functions using bioinformatics tools. The biological functions of DEPs included roles in photosynthesis, protein folding, antioxidant mechanism and metabolic processes, which responded differentially at each time point of drought treatment. To examine further transcriptional expression of the genes that code identified protein, quantitative real time PCR (qRT-PCR) was performed. Identified proteins will contribute to the studies involving development of drought-resistant crop species and lead to the delineation of molecular mechanisms in drought response.
      PubDate: 2017-08-01
      DOI: 10.1007/s11103-017-0628-2
      Issue No: Vol. 94, No. 6 (2017)
       
  • A novel AP2/ERF family transcription factor from Glycine soja , GsERF71,
           is a DNA binding protein that positively regulates alkaline stress
           tolerance in Arabidopsis
    • Authors: Yang Yu; Xiangbo Duan; Xiaodong Ding; Chao Chen; Dan Zhu; Kuide Yin; Lei Cao; Xuewei Song; Pinghui Zhu; Qiang Li; Zaib_un Nisa; Jiyang Yu; Jianying Du; Yu Song; Huiqing Li; Beidong Liu; Yanming Zhu
      Pages: 509 - 530
      Abstract: Key message Here we first found that GsERF71, an ERF factor from wild soybean could increase plant alkaline stress tolerance by up-regulating H+-ATPase and by modifing the accumulation of Auxin. Alkaline soils are widely distributed all over the world and greatly limit plant growth and development. In our previous transcriptome analyses, we have identified several ERF (ethylene-responsive factor) genes that responded strongly to bicarbonate stress in the roots of wild soybean G07256 (Glycine soja). In this study, we cloned and functionally characterized one of the genes, GsERF71. When expressed in epidermal cells of onion, GsERF71 localized to the nucleus. It can activate the reporters in yeast cells, and the C-terminus of 170 amino acids is essential for its transactivation activity. Yeast one-hybrid and EMSA assays indicated that GsERF71 specifically binds to the cis-acting elements of the GCC-box, suggesting that GsERF71 may participate in the regulation of transcription of the relevant biotic and abiotic stress-related genes. Furthermore, transgenic Arabidopsis plants overexpressing GsERF71 showed significantly higher tolerance to bicarbonate stress generated by NaHCO3 or KHCO3 than the wild type (WT) plants, i.e., the transgenic plants had greener leaves, longer roots, higher total chlorophyll contents and lower MDA contents. qRT-PCR and rhizosphere acidification assays indicated that the expression level and activity of H+-ATPase (AHA2) were enhanced in the transgenic plants under alkaline stress. Further analysis indicated that the expression of auxin biosynthetic genes and IAA contents were altered to a lower extent in the roots of transgenic plants than WT plants under alkaline stress in a short-term. Together, our data suggest that GsERF71 enhances the tolerance to alkaline stress by up-regulating the expression levels of H+-ATPase and by modifying auxin accumulation in transgenic plants.
      PubDate: 2017-07-01
      DOI: 10.1007/s11103-017-0623-7
      Issue No: Vol. 94, No. 4-5 (2017)
       
  • Overexpression of a peroxidase gene ( AtPrx64 ) of Arabidopsis thaliana in
           tobacco improves plant’s tolerance to aluminum stress
    • Authors: Yuanshuang Wu; Zhili Yang; Jingyi How; Huini Xu; Limei Chen; Kunzhi Li
      Abstract: Key message AtPrx64 is one of the peroxidases gene up-regulated in Al stress and has some functions in the formation of plant second cell wall. Its overexpression may improve plant tolerance to Al by some ways. Studies on its function under Al stress may help us to understand the mechanism of plant tolerance to Al stress. In Arabidopsis thaliana, the expressions of some genes (AtPrxs) encoding class III plant peroxidases have been found to be either up-regulated or down-regulated under aluminum (Al) stress. Among 73 genes that encode AtPrxs in Arabidopsis, AtPrx64 is always up-regulated by Al stress, suggesting this gene plays protective roles in response to such stress. In this study, transgenic tobacco plants were generated to examine the effects of overexpressing of AtPrx64 gene on the tolerance to Al stress. The results showed that overexpression of AtPrx64 gene increased the root growth and reduced the accumulation of Al and ROS in the roots. Compared with wild type controls, transgenic tobaccos had much less soluble proteins and malondialdehyde in roots and much more root citrate exudation. The activity of plasma membrane (PM) H+-ATPase, the phosphorylation of PM H+-ATPase and its interaction with 14-3-3 proteins increased in transgenic tobaccos; moreover, the content of lignin in root tips also increased. Taken together, these results showed that overexpression of AtPrx64 gene might enhance the tolerance of tobacco to Al stress.
      PubDate: 2017-08-16
      DOI: 10.1007/s11103-017-0644-2
       
  • CYP79 P450 monooxygenases in gymnosperms: CYP79A118 is associated with the
           formation of taxiphyllin in Taxus baccata
    • Authors: Katrin Luck; Qidong Jia; Meret Huber; Vinzenz Handrick; Gane Ka-Shu Wong; David R. Nelson; Feng Chen; Jonathan Gershenzon; Tobias G. Köllner
      Abstract: Key message Conifers contain P450 enzymes from the CYP79 family that are involved in cyanogenic glycoside biosynthesis. Cyanogenic glycosides are secondary plant compounds that are widespread in the plant kingdom. Their biosynthesis starts with the conversion of aromatic or aliphatic amino acids into their respective aldoximes, catalysed by N-hydroxylating cytochrome P450 monooxygenases (CYP) of the CYP79 family. While CYP79s are well known in angiosperms, their occurrence in gymnosperms and other plant divisions containing cyanogenic glycoside-producing plants has not been reported so far. We screened the transcriptomes of 72 conifer species to identify putative CYP79 genes in this plant division. From the seven resulting full-length genes, CYP79A118 from European yew (Taxus baccata) was chosen for further characterization. Recombinant CYP79A118 produced in yeast was able to convert l-tyrosine, l-tryptophan, and l-phenylalanine into p-hydroxyphenylacetaldoxime, indole-3-acetaldoxime, and phenylacetaldoxime, respectively. However, the kinetic parameters of the enzyme and transient expression of CYP79A118 in Nicotiana benthamiana indicate that l-tyrosine is the preferred substrate in vivo. Consistent with these findings, taxiphyllin, which is derived from l-tyrosine, was the only cyanogenic glycoside found in the different organs of T. baccata. Taxiphyllin showed highest accumulation in leaves and twigs, moderate accumulation in roots, and only trace accumulation in seeds and the aril. Quantitative real-time PCR revealed that CYP79A118 was expressed in plant organs rich in taxiphyllin. Our data show that CYP79s represent an ancient family of plant P450s that evolved prior to the separation of gymnosperms and angiosperms. CYP79A118 from T. baccata has typical CYP79 properties and its substrate specificity and spatial gene expression pattern suggest that the enzyme contributes to the formation of taxiphyllin in this plant species.
      PubDate: 2017-08-09
      DOI: 10.1007/s11103-017-0646-0
       
  • The MEDIATOR genes MED12 and MED13 control Arabidopsis root system
           configuration influencing sugar and auxin responses
    • Authors: Javier Raya-González; Jesús Salvador López-Bucio; José Carlos Prado-Rodríguez; León Francisco Ruiz-Herrera; Ángel Arturo Guevara-García; José López-Bucio
      Abstract: Key message Arabidopsis med12 and med13 mutants exhibit shoot and root phenotypes related to an altered auxin homeostasis. Sucrose supplementation reactivates both cell division and elongation in primary roots as well as auxin-responsive and stem cell niche gene expression in these mutants. An analysis of primary root growth of WT, med12, aux1-7 and med12 aux1 single and double mutants in response to sucrose and/or N-1-naphthylphthalamic acid (NPA) placed MED12 upstream of auxin transport for the sugar modulation of root growth. The MEDIATOR (MED) complex plays diverse functions in plant development, hormone signaling and biotic and abiotic stress tolerance through coordination of transcription. Here, we performed genetic, developmental, molecular and pharmacological analyses to characterize the role of MED12 and MED13 on the configuration of root architecture and its relationship with auxin and sugar responses. Arabidopsis med12 and med13 single mutants exhibit shoot and root phenotypes consistent with altered auxin homeostasis including altered primary root growth, lateral root development, and root hair elongation. MED12 and MED13 were required for activation of cell division and elongation in primary roots, as well as auxin-responsive and stem cell niche gene expression. Remarkably, most of these mutant phenotypes were rescued by supplying sucrose to the growth medium. The growth response of primary roots of WT, med12, aux1-7 and med12 aux1 single and double mutants to sucrose and application of auxin transport inhibitor N-1-naphthylphthalamic acid (NPA) revealed the correlation of med12 phenotype with the activity of the auxin intake permease and suggests that MED12 acts upstream of AUX1 in the root growth response to sugar. These data provide compelling evidence that MEDIATOR links sugar sensing to auxin transport and distribution during root morphogenesis.
      PubDate: 2017-08-05
      DOI: 10.1007/s11103-017-0647-z
       
  • Bypassing miRNA-mediated gene regulation under drought stress: alternative
           splicing affects CSD1 gene expression
    • Authors: So-Yon Park; Elizabeth Grabau
      Abstract: Key message The binding site for miR398 in an isoform of Cu/Zn superoxide dismutase (CSD1) is eliminated by alternative splicing to bypass miR398-mediated gene down-regulation under drought stress. MicroRNA (miRNA) binding sites (MBSs) are frequently interrupted by introns and therefore require proper splicing to generate functional MBSs in target transcripts. MBSs can also be excluded during splicing of pre-messenger RNA, leading to different regulation among isoforms. Previous studies have shown that levels of Cu/Zn superoxide dismutase (CSD) are down-regulated by miR398. In this study, sequences and transcript levels of peanut CSD1 isoforms (AhCSD1-1, AhCSD1-2.1, and AhCSD1-2.2) were analyzed under the drought stress. Results demonstrated that a miR398 binding site is eliminated in AhCSD1-2.2 as a consequence of alternative splicing, which bypasses miRNA-mediated down-regulation under drought stress. This alternative isoform was not only identified in peanut but also in soybean and Arabidopsis. In addition, transgenic Arabidopsis plants expressing AhCSD1 were more tolerant to osmotic stress. We hypothesize that the level of AhCSD1 is increased to allow diverse plant responses to overcome environmental challenges even in the presence of increased miR398 levels. These findings suggest that studies on the role of alternatively spliced MBSs affecting transcript levels are important for understanding plant stress responses.
      PubDate: 2017-08-03
      DOI: 10.1007/s11103-017-0642-4
       
  • Phytodetoxification of TNT by transplastomic tobacco ( Nicotiana tabacum )
           expressing a bacterial nitroreductase
    • Authors: Long Zhang; Elizabeth L. Rylott; Neil C. Bruce; Stuart E. Strand
      Abstract: Key message Expression of the bacterial nitroreductase gene, nfsI, in tobacco plastids conferred the ability to detoxify TNT. The toxic pollutant 2,4,6-trinitrotoluene (TNT) is recalcitrant to degradation in the environment. Phytoremediation is a potentially low cost remediation technique that could be applied to soil contaminated with TNT; however, progress is hindered by the phytotoxicity of this compound. Previous studies have demonstrated that plants transformed with the bacterial nitroreductase gene, nfsI have increased ability to tolerate and detoxify TNT. It has been proposed that plants engineered to express nfsI could be used to remediate TNT on military ranges, but this could require steps to mitigate transgene flow to wild populations. To address this, we have developed nfsI transplastomic tobacco (Nicotiana tabacum L.) to reduce pollen-borne transgene flow. Here we have shown that when grown on solid or liquid media, the transplastomic tobacco expressing nfsI were significantly more tolerant to TNT, produced increased biomass and removed more TNT from the media than untransformed plants. Additionally, transplastomic plants expressing nfsI regenerated with high efficiency when grown on medium containing TNT, suggesting that nfsI and TNT could together be used to provide a selectable screen for plastid transformation.
      PubDate: 2017-07-31
      DOI: 10.1007/s11103-017-0639-z
       
  • Evaluation of the mature grain phytase candidate HvPAPhy_a gene in barley
           ( Hordeum vulgare L.) using CRISPR/Cas9 and TALENs
    • Authors: Inger B. Holme; Toni Wendt; Javier Gil-Humanes; Lise C. Deleuran; Colby G. Starker; Daniel F. Voytas; Henrik Brinch-Pedersen
      Abstract: Abstract In the present study, we utilized TALEN- and CRISPR/Cas9-induced mutations to analyze the promoter of the barley phytase gene HvPAPhy_a. The purpose of the study was dual, validation of the PAPhy_a enzyme as the main contributor of the mature grain phytase activity (MGPA), as well as validating the importance of a specific promoter region of the PAPhy_a gene which contains three overlapping cis-acting regulatory elements (GCN4, Skn1 and the RY-element) known to be involved in gene expression during grain filling. The results confirm that the barley PAPhy_a enzyme is the main contributor to the MGPA as grains of knock-out lines show very low MGPA. Additionally, the analysis of the HvPAPhy_a promoter region containing the GCN4/Skn1/RY motif highlights its importance for HvPAPhy_a expression as the MGPA in grains of plant lines with mutations within this motif is significantly reduced. Interestingly, lines with deletions located downstream of the motif show even lower MGPA levels, indicating that the GCN4/SKn1/RY motif is not the only element responsible for the level of PAPhy_a expression during grain maturation. Mutant grains with very low MPGA showed delayed germination as compared to grains of wild type barley. As grains with high levels of preformed phytases would provide more readily available phosphorous needed for a fast germination, this indicates that faster germination may be implicated in the positive selection of the ancient PAPhy gene duplication that lead to the creation of the PAPhy_a gene.
      PubDate: 2017-07-28
      DOI: 10.1007/s11103-017-0640-6
       
  • A novel family of proline/serine-rich proteins, which are phospho-targets
           of stress-related mitogen-activated protein kinases, differentially
           regulates growth and pathogen defense in Arabidopsis thaliana
    • Authors: Mieder Anthony Thomas Palm-Forster; Lennart Eschen-Lippold; Joachim Uhrig; Dierk Scheel; Justin Lee
      Abstract: Abstract The molecular actions of mitogen-activated protein kinases (MAPKs) are ultimately accomplished by the substrate proteins where phosphorylation affects their molecular properties and function(s), but knowledge regarding plant MAPK substrates is currently still fragmentary. Here, we uncovered a previously uncharacterized protein family consisting of three proline/serine-rich proteins (PRPs) that are substrates of stress-related MAPKs. We demonstrated the importance of a MAPK docking domain necessary for protein–protein interaction with MAPKs and consequently also for phosphorylation. The main phosphorylated site was mapped to a residue conserved between all three proteins, which when mutated to a non-phosphorylatable form, differentially affected their protein stability. Together with their distinct gene expression patterns, this differential accumulation of the three proteins upon phosphorylation probably contributes to their distinct function(s). Transgenic over-expression of PRP, the founding member, led to plants with enhanced resistance to Pseudomonas syringae pv. tomato DC3000. Older plants of the over-expressing lines have curly leaves and were generally smaller in stature. This growth phenotype was lost in plants expressing the phosphosite variant, suggesting a phosphorylation-dependent effect. Thus, this novel family of PRPs may be involved in MAPK regulation of plant development and / or pathogen resistance responses. As datamining associates PRP expression profiles with hypoxia or oxidative stress and PRP-overexpressing plants have elevated levels of reactive oxygen species, PRP may connect MAPK and oxidative stress signaling.
      PubDate: 2017-07-28
      DOI: 10.1007/s11103-017-0641-5
       
  • Comparative analysis of Histone modifications and DNA methylation at OsBZ8
           locus under salinity stress in IR64 and Nonabokra rice varieties
    • Authors: Amit Paul; Pratiti Dasgupta; Dipan Roy; Shubho Chaudhuri
      Abstract: Abstract Rice being an important cereal crop is highly sensitive to salinity stress causing growth retardation and loss in productivity. However, certain rice genotypes like Nonabokra and Pokkali show a high level of tolerance towards salinity stress compared to IR64 variety. This differential response of tolerant varieties towards salinity stress may be a cumulative effect of genetic and epigenetic factors. In this study, we have compared the salinity-induced changes in chromatin modifications at the OsBZ8 locus in salt-tolerant Nonabokra and salt-sensitive IR64 rice varieties. Expression analysis indicates that the OsBZ8 gene is highly induced in Nonabokra plants even in the absence of salt stress, whereas in IR64, the expression significantly increases only during salt stress. Sequence analysis and nucleosomal arrangement within the region −2000 to +1000 of OsBZ8 gene show no difference between the two rice varieties. However, there was a considerable difference in histone modifications and DNA methylation at the locus between these varieties. In Nonabokra, the upstream region was hyperacetylated at H3K9 and H3K27, and this acetylation did not change during salt stress. However, in IR64, histone acetylation was observed only during salt stress. Moreover, the upstream region of OsBZ8 gene has highly dynamic nucleosome arrangement in Nonabokra, compared to IR64. Furthermore, loss of DNA methylation was observed at OsBZ8 locus in Nonabokra control plants along with low H3K27me3 and high H3K4me3. Control IR64 plants show high DNA methylation and enriched H3K27me3. Collectively these results indicate a significant difference in chromatin modifications between the rice varieties that regulates differential expression of OsBZ8 gene during salt stress.
      PubDate: 2017-07-24
      DOI: 10.1007/s11103-017-0636-2
       
  • Low genetic diversity and functional constraint of miRNA genes
           participating pollen–pistil interaction in rice
    • Authors: Kun Wang; Xin Wang; Ming Li; Tao Shi; Pingfang Yang
      Abstract: Key message In this study, we sequenced and analyzed the expression and evolution of rice miRNA genes participating pollen-pistil interaction that is crucial to rice yield. Pollen–pistil interaction is an essential reproductive process for all flowering plants. While microRNAs (miRNAs) are important noncoding small RNAs that regulate mRNA levels in eukaryotic cells, there is little knowledge about which miRNAs involved in the early stages of pollen–pistil interaction in rice and how they evolve under this conserved process. In this study, we sequenced the small RNAs in rice from unpollinated pistil (R0), pistil from 5 min and 15 min after pollination, respectively, to identify known and novel miRNAs that are involved in this process. By comparing the corresponding mRNA-seq dataset, we identified a group of miRNAs with strong negative expression pattern with their target genes. Further investigation of all miRNA loci (MIRNAs) across 1083 public rice accessions revealed significantly reduced genetic diversity in MIRNAs with strong negative expression of their targets when comparing to those with little or no impact on targets during pollen–pistil interaction. Annotation of targets suggested that those MIRNAs with strong impact on targets were pronounced in cell wall related processes such as xylan metabolism. Additionally, plant conserved miRNAs, such as those with functions in gibberellic acid, auxin and nitrate signaling, were also with strong negative expression of their targets. Overall, our analyses identified key miRNAs participating pollen–pistil interaction and their evolutionary patterns in rice, which can facilitate the understanding of molecular mechanisms associated with seed setting.
      PubDate: 2017-07-22
      DOI: 10.1007/s11103-017-0638-0
       
  • Metabolic profiles of flooding-tolerant mechanism in early-stage soybean
           responding to initial stress
    • Authors: Xin Wang; Wei Zhu; Akiko Hashiguchi; Minoru Nishimura; Jingkui Tian; Setsuko Komatsu
      Abstract: Key message Metabolomic analysis of flooding-tolerant mutant and abscisic acid-treated soybeans suggests that accumulated fructose might play a role in initial flooding tolerance through regulation of hexokinase and phosphofructokinase. Soybean is sensitive to flooding stress, which markedly reduces plant growth. To explore the mechanism underlying initial-flooding tolerance in soybean, mass spectrometry-based metabolomic analysis was performed using flooding-tolerant mutant and abscisic-acid treated soybeans. Among the commonly-identified metabolites in both flooding-tolerant materials, metabolites involved in carbohydrate and organic acid displayed same profile at initial-flooding stress. Sugar metabolism was highlighted in both flooding-tolerant materials with the decreased and increased accumulation of sucrose and fructose, respectively, compared to flooded soybeans. Gene expression of hexokinase 1 was upregulated in flooded soybean; however, it was downregulated in both flooding-tolerant materials. Metabolites involved in carbohydrate/organic acid and proteins related to glycolysis/tricarboxylic acid cycle were integrated. Increased protein abundance of phosphofructokinase was identified in both flooding-tolerant materials, which was in agreement with its enzyme activity. Furthermore, sugar metabolism was pointed out as the tolerant-responsive process at initial-flooding stress with the integration of metabolomics, proteomics, and transcriptomics. Moreover, application of fructose declined the increased fresh weight of plant induced by flooding stress. These results suggest that fructose might be the critical metabolite through regulation of hexokinase and phosphofructokinase to confer initial-flooding stress in soybean.
      PubDate: 2017-07-21
      DOI: 10.1007/s11103-017-0635-3
       
  • A MDR transporter contributes to the different extracellular production of
           sesquiterpene pyridine alkaloids between adventitious root and hairy root
           liquid cultures of Tripterygium wilfordii Hook.f.
    • Authors: Guo-peng Miao; Juan Han; Ji-feng Zhang; Chuan-shu Zhu; Xing Zhang
      Abstract: Key message TwMDR1 transports sesquiterpene pyridine alkaloids, wilforine and wilforgine, into the hairy roots of T. wilfordii Hook.f. resulting in low secretion ratio of alkaloids. Hairy roots (HRs) exhibit high growth rate and biochemical and genetic stability. However, varying secondary metabolites in HR liquid cultures mainly remain in root tissues, and this condition may affect cell growth and cause inconvenience in downstream extraction. Studies pay less attention to adventitious root (AR) liquid cultures though release ratio of some metabolites in AR liquid cultures is significantly higher than that of HR. In Tripterygium wilfordii Hook.f., release ratio of wilforine in AR liquid cultures reached 92.75 and 13.32% in HR on day 15 of culture. To explore potential roles of transporters in this phenomenon, we cloned and functionally identified a multidrug resistance (MDR) transporter, TwMDR1, which shows high expression levels in HRs and is correlated to transmembrane transportation of alkaloids. Nicotiana tabacum cells with overexpressed TwMDR1 efficiently transported wilforine and wilforgine in an inward direction. To further prove the feasibility of genetically engineered TwMDR1 and improve alkaloid production, we performed a transient RNAi experiment on TwMDR1 in T. wilfordii Hook.f. suspension cells. Results indicated that release ratios of wilforine and wilforgine increased by 1.94- and 1.64-folds compared with that of the control group, respectively. This study provides bases for future studies that aim at increasing secretion ratios of alkaloids in root liquid cultures in vitro.
      PubDate: 2017-07-21
      DOI: 10.1007/s11103-017-0634-4
       
  • Identification of a seed coat-specific promoter fragment from the
           Arabidopsis MUCILAGE-MODIFIED4 gene
    • Authors: Gillian H. Dean; Zhaoqing Jin; Lin Shi; Elahe Esfandiari; Robert McGee; Kylie Nabata; Tiffany Lee; Ljerka Kunst; Tamara L. Western; George W. Haughn
      Abstract: Key message The Arabidopsis seed coat-specific promoter fragment described is an important tool for basic and applied research in Brassicaceae species. During differentiation, the epidermal cells of the Arabidopsis seed coat produce and secrete large quantities of mucilage. On hydration of mature seeds, this mucilage becomes easily accessible as it is extruded to form a tightly attached halo at the seed surface. Mucilage is composed mainly of pectin, and also contains the key cell wall components cellulose, hemicellulose, and proteins, making it a valuable model for studying numerous aspects of cell wall biology. Seed coat-specific promoters are an important tool that can be used to assess the effects of expressing biosynthetic enzymes and diverse cell wall-modifying proteins on mucilage structure and function. Additionally, they can be used for production of easily accessible recombinant proteins of commercial interest. The MUCILAGE-MODIFIED4 (MUM4) gene is expressed in a wide variety of plant tissues and is strongly up-regulated in the seed coat during mucilage synthesis, implying the presence of a seed coat-specific region in its promoter. Promoter deletion analysis facilitated isolation of a 308 base pair sequence (MUM4 0.3Pro ) that directs reporter gene expression in the seed coat cells of both Arabidopsis and Camelina sativa, and is regulated by the same transcription factor cascade as endogenous MUM4. Therefore, MUM4 0.3Pro is a promoter fragment that serves as a new tool for seed coat biology research.
      PubDate: 2017-07-20
      DOI: 10.1007/s11103-017-0631-7
       
  • UBIQUITIN-SPECIFIC PROTEASES function in plant development and stress
           responses
    • Authors: Huapeng Zhou; Jinfeng Zhao; Jingqing Cai; Suyash B. Patil
      Abstract: Key message UBIQUITIN-SPECIFIC PROTEASES play important roles in plant development and stress responses. Protein ubiquitination and deubiquitination are reversible processes, which can modulate the stability, activity as well as subcellular localization of the substrate proteins. UBIQUITIN-SPECIFIC PROTEASE (UBP) protein family participates in protein deubiquitination. Members of UBP family are involved in a variety of physiological processes in plants, as evidenced by their functional characterization in model plant Arabidopsis and other plants. UBPs are conserved in plants and distinct UBPs function in different regulatory processes, although functional redundancies exist between some members. Here we briefly reviewed recent advances in understanding the biological functions of UBP protein family in Arabidopsis, particularly the molecular mechanisms by which UBPs regulate plant development and stress responses. We believe that elucidation of UBPs function and regulation in Arabidopsis will provide new insights about protein deubiquitination and might shed light on the understanding of the mechanistic roles of UBPs in general, which will definitely contribute to crop improvement in agriculture.
      PubDate: 2017-07-10
      DOI: 10.1007/s11103-017-0633-5
       
  • Bacterial production and reconstitution in proteoliposomes of Solanum
           
    • Authors: Teresa Maria Rosaria Regina; Michele Galluccio; Mariafrancesca Scalise; Lorena Pochini; Cesare Indiveri
      Abstract: Key message The vacuolar SlCAT2 was cloned, over-produced in E. coli and reconstituted in proteoliposomes. Arg, Ornithine and Lys were identified as substrates. Unexpectedly, also the organic cations Tetraethylammonium and Acetylcholine were transported indicating involvement of SlCAT2 in signaling. In land plants several transporters are involved in ion and metabolite flux across membranes of cells or intracellular organelles. The vacuolar amino acid transporter CAT2 from Solanum lycopersicum was investigated in this work. SlCAT2 was cloned from tomato flower cDNA, over-produced in Escherichia coli and purified by Nichel-chelating chromatography. For functional studies, the transporter was reconstituted in proteoliposomes. Competence of SlCAT2 for Arg transport was demonstrated measuring uptake of [3H]Arg in proteoliposomes which was trans-stimulated by internal Arg or ornithine. Uptake of [3H]Ornithine and [3H]Lys was also detected at lower efficiency with respect to [3H]Arg. Transport was activated by the presence of intraliposomal ATP suggesting regulation by the nucleotide. The prototype for organic cations tetraethylammonium (TEA) was also transported by SlCAT2. However, scarce reciprocal inhibition between TEA and Arg was found, while the biguanide metformin was able to strongly inhibit uptake of both substrates. These findings suggest that amino acids and organic cations may interact with the transporter through different functional groups some of which are common for the two types of substrates. Interestingly, reconstituted SlCAT2 showed competence for acetylcholine transport, which was also inhibited by metformin. Kinetics of Arg and Ach transport were performed from which Km values of 0.29 and 0.79 mM were derived, respectively.
      PubDate: 2017-07-10
      DOI: 10.1007/s11103-017-0632-6
       
  • A comparative genomic and transcriptomic analysis at the level of isolated
           root hair cells reveals new conserved root hair regulatory elements
    • Authors: Zhenzhen Qiao; Lise Pingault; Prince Zogli; Micaela Langevin; Niccole Rech; Andrew Farmer; Marc Libault
      Abstract: Key message A comparative transcriptomic and genomic analysis between Arabidopsis thaliana and Glycine max root hair genes reveals the evolution of the expression of plant genes after speciation and whole genome duplication. Our understanding of the conservation and divergence of the expression patterns of genes between plant species is limited by the quality of the genomic and transcriptomic resources available. Specifically, the transcriptomes generated from plant organs are the reflection of the contribution of the different cell types composing the samples weighted by their relative abundances in the sample. These contributions can vary between plant species leading to the generation of datasets which are difficult to compare. To gain a deeper understanding of the evolution of gene transcription in and between plant species, we performed a comparative transcriptomic and genomic analysis at the level of one single plant cell type, the root hair cell, and between two model plants: Arabidopsis (Arabidopsis thaliana) and soybean (Glycine max). These two species, which diverged 90 million years ago, were selected as models based on the large amount of genomic and root hair transcriptomic information currently available. Our analysis revealed in detail the transcriptional divergence and conservation between soybean paralogs (i.e., the soybean genome is the product of two successive whole genome duplications) and between Arabidopsis and soybean orthologs in this single plant cell type. Taking advantage of this evolutionary study, we combined bioinformatics, molecular, cellular and microscopic tools to characterize plant promoter sequences and the discovery of two root hair regulatory elements (RHE1 and RHE2) consistently and specifically active in plant root hair cells.
      PubDate: 2017-07-07
      DOI: 10.1007/s11103-017-0630-8
       
  • Herbaspirillum rubrisubalbicans , a mild pathogen impairs growth of rice
           by augmenting ethylene levels
    • Authors: Glaucio Valdameri; Dayane Alberton; Vivian Rotuno Moure; Thiago Borba Kokot; Caroline Kukolj; Liziane Cristina Campos Brusamarello-Santos; Rose Adele Monteiro; Fabio de Oliveira Pedrosa; Emanuel Maltempi de Souza
      Abstract: Key message Herbaspirillum rubrisubalbicans decreases growth of rice. Inoculation of rice with H. rubrisubalbicans increased the ACCO mRNA levels and ethylene production. The H. rubrisubalbicans rice interactions were further characterized by proteomic approach. Herbaspirillum rubrisubalbicans is a well-known growth-promoting rhizobacteria that can also act as a mild phyto-pathogen. During colonisation of rice, RT-qPCR analyses showed that H. rubrisubalbicans up-regulates the methionine recycling pathway as well as phyto-siderophore synthesis genes. mRNA levels of ACC oxidase and ethylene levels also increased in rice roots but inoculation with H. rubrisubalbicans impaired growth of the rice plant. A proteomic approach was used to identify proteins specifically modulated by H. rubrisubalbicans in rice and amongst the differentially expressed proteins a V-ATPase and a 14-3-3 protein were down-regulated. Several proteins of H. rubrisubalbicans were identified, including the type VI secretion system effector Hcp1, suggesting that protein secretion play a role colonisation in rice. Finally, the alkyl hydroperoxide reductase, a primary scavenger of endogenous hydrogen peroxide was also identified. Monitoring the levels of reactive oxygen species in the epiphytic bacteria by flow cytometry revealed that H. rubrisubalbicans is subjected to oxidative stress, suggesting that the alkyl hydroperoxide reductase is an important regulator of redox homeostasis in plant-bacteria interactions.
      PubDate: 2017-07-03
      DOI: 10.1007/s11103-017-0629-1
       
 
 
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