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https://www.readbyqxmd.com/read/29342073/structure-elucidation-of-unknown-metabolites-in-metabolomics-by-combined-nmr-and-ms-ms-prediction
#1
Rene M Boiteau, David W Hoyt, Carrie D Nicora, Hannah A Kinmonth-Schultz, Joy K Ward, Kerem Bingol
We introduce a cheminformatics approach that combines highly selective and orthogonal structure elucidation parameters; accurate mass, MS/MS (MS²), and NMR into a single analysis platform to accurately identify unknown metabolites in untargeted studies. The approach starts with an unknown LC-MS feature, and then combines the experimental MS/MS and NMR information of the unknown to effectively filter out the false positive candidate structures based on their predicted MS/MS and NMR spectra. We demonstrate the approach on a model mixture, and then we identify an uncatalogued secondary metabolite in Arabidopsis thaliana...
January 17, 2018: Metabolites
https://www.readbyqxmd.com/read/29341856/kix-domain-of-atmed15a-a-mediator-subunit-of-arabidopsis-is-required-for-its-interaction-with-different-proteins
#2
Vinay Kumar, Mohd Waseem, Nidhi Dwivedi, Sourobh Maji, Angad Kumar, Jitendra K Thakur
Med15 is an important subunit of Mediator tail module and is characterized by a KIX domain present in the amino terminal. In yeast and metazoans, Med15 KIX domain has been found to interact with various transcription factors, regulating several processes including carbohydrate metabolism, lipogenesis, stress response and multidrug resistance. Mechanism of Med15 functioning in Arabidopsis is largely unknown. In this study, interactome of Arabidopsis Med15, AtMed15a, was characterized. We found 45 proteins that interact with AtMed15a KIX domain, including 11 transcription factors, 3 single strand nucleic acid-binding proteins and 1 splicing factor...
January 17, 2018: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/29341173/strigolactones-positively-regulate-chilling-tolerance-in-pea-and-in-arabidopsis
#3
James W Cooper, Yan Hu, Leila Beyyoudh, H Yildiz Dasgan, Karl Kunert, Christine A Beveridge, Christine H Foyer
Strigolactones (SL) fulfil important roles in plant development and stress tolerance. Here we characterised the role of SL in the dark chilling tolerance of pea and Arabidopsis by analysis of mutants that are defective in either SL synthesis or signalling. Pea mutants (rms3, rms4, rms5) had significantly greater shoot branching with higher leaf chlorophyll a/b ratios and carotenoid contents than the wild type. Exposure to dark chilling significantly decreased shoot fresh weights but increased leaf numbers in all lines...
January 17, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29341143/loss-of-alkaline-ceramidase-inhibits-autophagy-in-arabidopsis-and-plays-an-important-role-during-environmental-stress-response
#4
Ping Zheng, Jian-Xin Wu, Sunil Kumar Sahu, Hong-Yun Zeng, Li-Qun Huang, Zhe Liu, Shi Xiao, Nan Yao
Sphingolipids, a class of bioactive lipids found in cell membranes, can modulate the biophysical properties of the membranes and play a critical role in signal transduction. Sphingolipids are involved in autophagy in humans and yeast, but their role in autophagy in plants is not well understood. In this study, we reported that the AtACER, an alkaline ceramidase that hydrolyzes ceramide to LCB, functions in autophagy process in Arabidopsis. Our empirical data showed that the loss of AtACER inhibited autophagy, while its overexpression promoted autophagy under nutrient, salinity, and oxidative stresses...
January 17, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29340952/rfathm6a-a-new-tool-for-predicting-m6a-sites-in-arabidopsis-thaliana
#5
Xiaofeng Wang, Renxiang Yan
We curated a reliable dataset of m6A sites in Arabidopsis thaliana, built competitive models for predicting m6A sites, extracted predominant rules from the prediction models and analyzed the most important features. In biological RNA, approximately 150 chemical modifications have been discovered, of which N6-methyladenine (m6A) is the most prevalent and abundant. This modification plays an essential role in a myriad of biological mechanisms and regulates RNA localization, nuclear export, translation, stability, alternative splicing, and other processes...
January 16, 2018: Plant Molecular Biology
https://www.readbyqxmd.com/read/29340752/the-effect-of-indehiscent-point-mutations-on-silique-shatter-resistance-in-oilseed-rape-brassica-napus
#6
Janina Braatz, Hans-Joachim Harloff, Nazgol Emrani, Chirlon Elisha, Lars Heepe, Stanislav N Gorb, Christian Jung
This study elucidates the influence of indehiscent mutations on rapeseed silique shatter resistance. A phenotype with enlarged replum-valve joint area and altered cell dimensions in the dehiscence zone is described. Silique shattering is a major factor reducing the yield stability of oilseed rape (Brassica napus). Attempts to improve shatter resistance often include the use of mutations in target genes identified from Arabidopsis (Arabidopsis thaliana). A variety of phenotyping methods assessing the level of shatter resistance were previously described...
January 16, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29340613/biomass-increase-under-zinc-deficiency-caused-by-delay-of-early-flowering-in-arabidopsis
#7
Xiaochao Chen, Uwe Ludewig
Plants generally produce more biomass when all nutrients are available in sufficient amounts. In addition to environmental constraints, genetic and developmental factors, such as the transition from vegetative to reproductive growth, restrict maximal yield. Here we report the peculiar observation that a subset of Arabidopsis thaliana accessions produced larger shoot rosette diameters when grown in zinc (Zn)-deficient conditions, compared with Zn-sufficient conditions. This was associated with early flowering that restricted the leaf length under Zn sufficiency...
January 11, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29339969/a-new-toolset-for-protein-expression-and-subcellular-localization-studies-in-citrus-and-its-application-to-citrus-tristeza-virus-proteins
#8
Amit Levy, Choaa El-Mochtar, Chunxia Wang, Michael Goodin, Vladimir Orbovic
Background: Transient gene expression is a powerful tool to study gene function in plants. In citrus, Agrobacterium transformation is the method of choice for transient expression studies, but this method does not work efficiently with many gene constructs, and there is a need for a more robust transient expression system in citrus leaves. Biolistic particle delivery is an alternative to Agrobacterium transformation, and in some plants, such as Arabidopsis, gives higher transformation rates in leaf tissues than Agrobacterium...
2018: Plant Methods
https://www.readbyqxmd.com/read/29339507/large-scale-comparative-epigenomics-reveals-hierarchical-regulation-of-non-cg-methylation-in-arabidopsis
#9
Yu Zhang, C Jake Harris, Qikun Liu, Wanlu Liu, Israel Ausin, Yanping Long, Lidan Xiao, Li Feng, Xu Chen, Yubin Xie, Xinyuan Chen, Lingyu Zhan, Suhua Feng, Jingyi Jessica Li, Haifeng Wang, Jixian Zhai, Steven E Jacobsen
Genome-wide characterization by next-generation sequencing has greatly improved our understanding of the landscape of epigenetic modifications. Since 2008, whole-genome bisulfite sequencing (WGBS) has become the gold standard for DNA methylation analysis, and a tremendous amount of WGBS data has been generated by the research community. However, the systematic comparison of DNA methylation profiles to identify regulatory mechanisms has yet to be fully explored. Here we reprocessed the raw data of over 500 publicly available Arabidopsis WGBS libraries from various mutant backgrounds, tissue types, and stress treatments and also filtered them based on sequencing depth and efficiency of bisulfite conversion...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29339505/nonenzymatic-release-of-n7-methylguanine-channels-repair-of-abasic-sites-into-an-ap-endonuclease-independent-pathway-in-arabidopsis
#10
Casimiro Barbado, Dolores Córdoba-Cañero, Rafael R Ariza, Teresa Roldán-Arjona
Abasic (apurinic/apyrimidinic, AP) sites in DNA arise from spontaneous base loss or by enzymatic removal during base excision repair. It is commonly accepted that both classes of AP site have analogous biochemical properties and are equivalent substrates for AP endonucleases and AP lyases, although the relative roles of these two types of enzymes are not well understood. We provide here genetic and biochemical evidence that, in Arabidopsis, AP sites generated by spontaneous loss of N7-methylguanine (N7-meG) are exclusively repaired through an AP endonuclease-independent pathway initiated by FPG, a bifunctional DNA glycosylase with AP lyase activity...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29339437/spr2-protects-minus-ends-to-promote-severing-and-reorientation-of-plant-cortical-microtubule-arrays
#11
Masayoshi Nakamura, Jelmer J Lindeboom, Marco Saltini, Bela M Mulder, David W Ehrhardt
The cortical microtubule arrays of higher plants are organized without centrosomes and feature treadmilling polymers that are dynamic at both ends. The control of polymer end stability is fundamental for the assembly and organization of cytoskeletal arrays, yet relatively little is understood about how microtubule minus ends are controlled in acentrosomal microtubule arrays, and no factors have been identified that act at the treadmilling minus ends in higher plants. Here, we identify Arabidopsis thaliana SPIRAL2 (SPR2) as a protein that tracks minus ends and protects them against subunit loss...
January 16, 2018: Journal of Cell Biology
https://www.readbyqxmd.com/read/29337129/effect-of-amino-acid-substitution-of-caprice-on-cell-to-cell-movement-ability-in-arabidopsis-root-epidermis
#12
Rumi Tominaga-Wada, Takuji Wada
An R3-type MYB transcription factor, CAPRICE (CPC), is known to promote root hair cell differentiation in Arabidopsis root epidermis. The CPC protein moves from non-hair cells to the neighboring cells, and acts as an inducer of root hair formation. In contrast, we previously showed that the CPC homolog, ENHANCER OF TRY AND CPC1 (ETC1), does not move between the root epidermal cells. To clarify the critical difference in the cell-to-cell movement ability of CPC and ETC1 proteins, we generated five different chimeras of CPC and ETC1...
January 11, 2018: Developmental Biology
https://www.readbyqxmd.com/read/29337078/circadian-waves-of-transcriptional-repression-shape-pif-regulated-photoperiod-responsive-growth-in-arabidopsis
#13
Guiomar Martín, Arnau Rovira, Nil Veciana, Judit Soy, Gabriela Toledo-Ortiz, Charlotte M M Gommers, Marc Boix, Rossana Henriques, Eugenio G Minguet, David Alabadí, Karen J Halliday, Pablo Leivar, Elena Monte
Plants coordinate their growth and development with the environment through integration of circadian clock and photosensory pathways. In Arabidopsis thaliana, rhythmic hypocotyl elongation in short days (SD) is enhanced at dawn by the basic-helix-loop-helix (bHLH) transcription factors PHYTOCHROME-INTERACTING FACTORS (PIFs) directly inducing expression of growth-related genes [1-6]. PIFs accumulate progressively during the night and are targeted for degradation by active phytochromes in the light, when growth is reduced...
January 9, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29337075/brassinosteroids-dominate-hormonal-regulation-of-plant-thermomorphogenesis-via-bzr1
#14
Carla Ibañez, Carolin Delker, Cristina Martinez, Katharina Bürstenbinder, Philipp Janitza, Rebecca Lippmann, Wenke Ludwig, Hequan Sun, Geo Velikkakam James, Maria Klecker, Alexandra Grossjohann, Korbinian Schneeberger, Salome Prat, Marcel Quint
Thermomorphogenesis is defined as the suite of morphological changes that together are likely to contribute to adaptive growth acclimation to usually elevated ambient temperature [1, 2]. While many details of warmth-induced signal transduction are still elusive, parallels to light signaling recently became obvious (reviewed in [3]). It involves photoreceptors that can also sense changes in ambient temperature [3-5] and act, for example, by repressing protein activity of the central integrator of temperature information PHYTOCHROME-INTERACTING FACTOR 4 (PIF4 [6])...
January 5, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29335919/inter-and-intracellular-colonization-of-arabidopsis-roots-by-endophytic-actinobacteria-and-the-impact-of-plant-hormones-on-their-antimicrobial-activity
#15
Anne van der Meij, Joost Willemse, Martinus A Schneijderberg, René Geurts, Jos M Raaijmakers, Gilles P van Wezel
Many actinobacteria live in close association with eukaryotes such as fungi, insects, animals and plants. Plant-associated actinobacteria display (endo)symbiotic, saprophytic or pathogenic life styles, and can make up a substantial part of the endophytic community. Here, we characterised endophytic actinobacteria isolated from root tissue of Arabidopsis thaliana (Arabidopsis) plants grown in soil from a natural ecosystem. Many of these actinobacteria belong to the family of Streptomycetaceae with Streptomyces olivochromogenes and Streptomyces clavifer as well represented species...
January 15, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29335788/over-expression-of-a-grafting-responsive-gene-from-hickory-increases-abiotic-stress-tolerance-in-arabidopsis
#16
R M Saravana Kumar, Guocun Ji, Haipeng Guo, Liang Zhao, Bingsong Zheng
A grafting response gene CcPIP1;2 was cloned from hickory plant, further functional characterization of the gene for water transport activity and abiotic stress tolerances were carried out through heterologous expression in Xenopus and Arabidopsis. Plasma membrane intrinsic proteins (PIPs) are multifunctional channel proteins belonging to the membrane intrinsic protein (MIP) family. In this study, a grafting-responsive gene from hickory (CcPIP1;2) was cloned and functionally characterized. Application of non-selective water inhibitors (HgCl2 and phloretin) led to the death of grafted hickory plants at 30 days after grafting (DAG)...
January 15, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29335785/heterologous-expression-of-rice-9-cis-epoxycarotenoid-dioxygenase-4-osnced4-in-arabidopsis-confers-sugar-oversensitivity-and-drought-tolerance
#17
San-Gwang Hwang, Chia-Yun Lee, Ching-Shan Tseng
BACKGROUND: The 9-cis-epoxycarotenoid dioxygenases OsNCED4 was cloned from rice in conjunction with OsNCED 1-3 and 5, of which 3 has been shown to function in ABA biosynthesis and alteration of leaf morphology. In higher plants, NCEDs have been shown to be key enzymes controlling ABA biosynthesis and belong to a differentially expressed gene family. Aside from OsNCED3, it remains largely unknown if other OsNCED genes are involved in ABA biosynthesis in rice. Thus, transgenic Arabidopsis plants overexpressing OsNCED4 were generated in the 129B08/nced3 mutant background to explore OsNCED4 function in ABA biosynthesis...
January 15, 2018: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/29335590/direct-observation-of-the-effects-of-cellulose-synthesis-inhibitors-using-live-cell-imaging-of-cellulose-synthase-cesa-in-physcomitrella-patens
#18
Mai L Tran, Thomas W McCarthy, Hao Sun, Shu-Zon Wu, Joanna H Norris, Magdalena Bezanilla, Luis Vidali, Charles T Anderson, Alison W Roberts
Results from live cell imaging of fluorescently tagged Cellulose Synthase (CESA) proteins in Cellulose Synthesis Complexes (CSCs) have enhanced our understanding of cellulose biosynthesis, including the mechanisms of action of cellulose synthesis inhibitors. However, this method has been applied only in Arabidopsis thaliana and Brachypodium distachyon thus far. Results from freeze fracture electron microscopy of protonemal filaments of the moss Funaria hygrometrica indicate that a cellulose synthesis inhibitor, 2,6-dichlorobenzonitrile (DCB), fragments CSCs and clears them from the plasma membrane...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29335548/paternal-easirnas-regulate-parental-genome-dosage-in-arabidopsis
#19
German Martinez, Philip Wolff, Zhenxing Wang, Jordi Moreno-Romero, Juan Santos-González, Lei Liu Conze, Christopher DeFraia, R Keith Slotkin, Claudia Köhler
The regulation of parental genome dosage is of fundamental importance in animals and plants, as exemplified by X-chromosome inactivation and dosage compensation. The 'triploid block' is a classic example of dosage regulation in plants that establishes a reproductive barrier between species differing in chromosome number1,2. This barrier acts in the embryo-nourishing endosperm tissue and induces the abortion of hybrid seeds through a yet unknown mechanism 3 . Here we show that depletion of paternal epigenetically activated small interfering RNAs (easiRNAs) bypasses the triploid block in response to increased paternal ploidy in Arabidopsis thaliana...
January 15, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29335544/transposon-derived-small-rnas-triggered-by-mir845-mediate-genome-dosage-response-in-arabidopsis
#20
Filipe Borges, Jean-Sébastien Parent, Frédéric van Ex, Philip Wolff, German Martínez, Claudia Köhler, Robert A Martienssen
Chromosome dosage has substantial effects on reproductive isolation and speciation in both plants and animals, but the underlying mechanisms are largely obscure 1 . Transposable elements in animals can regulate hybridity through maternal small RNA 2 , whereas small RNAs in plants have been postulated to regulate dosage response via neighboring imprinted genes3,4. Here we show that a highly conserved microRNA in plants, miR845, targets the tRNAMet primer-binding site (PBS) of long terminal repeat (LTR) retrotransposons in Arabidopsis pollen, and triggers the accumulation of 21-22-nucleotide (nt) small RNAs in a dose-dependent fashion via RNA polymerase IV...
January 15, 2018: Nature Genetics
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