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Arabidopsis thaliana

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https://www.readbyqxmd.com/read/27912765/rna-seq-based-digital-gene-expression-analysis-reveals-modification-of-host-defense-responses-by-rice-stripe-virus-during-disease-symptom-development-in-arabidopsis
#1
Feng Sun, Peng Fang, Juan Li, Linlin Du, Ying Lan, Tong Zhou, Yongjian Fan, Wenbiao Shen, Yijun Zhou
BACKGROUND: Virus infection induces and suppresses host gene expression on a global level. Rice stripe virus (RSV) is the type species of the genus Tenuivirus and infects rice and Arabidopsis plants. Microarray-based and next generation sequencing-based transcriptomic approaches have been used to study rice-RSV interactions. However, our knowledge of the response of Arabidopsis plants to RSV infection is limited, and it requires further investigation to determine the similarities (or differences) in virus-host interactions between monocot and dicot hosts infected with RSV...
December 2, 2016: Virology Journal
https://www.readbyqxmd.com/read/27912180/radicals-formed-from-proton-loss-of-carotenoid-radical-cations-a-special-form-of-carotenoid-neutral-radical-occurring-in-photoprotection
#2
A Ligia Focsan, Lowell D Kispert
In an organized assembly in Arabidopsis thaliana plant, proton loss from the radical cation of zeaxanthin (Zea(+)) was found to occur under intense illumination, a possible component in photoprotection. A stable neutral radical is formed because of the favorable proton loss at C4(4') position(s) of the terminal ends of Zea(+) that extends the unpaired spin density distribution (notation Zea(4) or Zea(4') by symmetry). Proton loss from the radical cation of β-carotene (β-car(+)) to available proton acceptors was also detected in a PSII sample upon irradiation...
November 19, 2016: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/27911402/utilizing-the-ethylene-releasing-compound-2-chloroethylphosphonic-acid-as-a-tool-to-study-ethylene-response-in-bacteria
#3
Richard V Augimeri, Andrew J Varley, Janice L Strap
Ethylene (C2H4) is a gaseous phytohormone that is involved in numerous aspects of plant development, playing a dominant role in senescence and fruit ripening. Exogenous ethylene applied during early plant development triggers the triple response phenotype; a shorter and thicker hypocotyl with an exaggerated apical hook. Despite the intimate relationship between plants and bacteria, the effect of exogenous ethylene on bacteria has been greatly overlooked. This is partly due to the difficulty of controlling gaseous ethylene within the laboratory without specialized equipment...
November 10, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27910910/genome-wide-characterisation-and-expression-profile-of-the-grapevine-atl-ubiquitin-ligase-family-reveal-biotic-and-abiotic-stress-responsive-and-development-related-members
#4
Pietro Ariani, Alice Regaiolo, Arianna Lovato, Alejandro Giorgetti, Andrea Porceddu, Salvatore Camiolo, Darren Wong, Simone Castellarin, Elodie Vandelle, Annalisa Polverari
The Arabidopsis Tóxicos en Levadura (ATL) protein family is a class of E3 ubiquitin ligases with a characteristic RING-H2 Zn-finger structure that mediates diverse physiological processes and stress responses in plants. We carried out a genome-wide survey of grapevine (Vitis vinifera L.) ATL genes and retrieved 96 sequences containing the canonical ATL RING-H2 domain. We analysed their genomic organisation, gene structure and evolution, protein domains and phylogenetic relationships. Clustering revealed several clades, as already reported in Arabidopsis thaliana and rice (Oryza sativa), with an expanded subgroup of grapevine-specific genes...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910895/arabidopsis-thaliana-as-a-suitable-model-host-for-research-on-interactions-between-plant-and-foliar-nematodes-parasites-of-plant-shoot
#5
Dong-Wei Wang, Xiao-Fang Peng, Hui Xie, Chun-Ling Xu, De-Qiang Cheng, Jun-Yi Li, Wen-Jia Wu, Ke Wang
The rice white tip nematode (RWTN), Aphelenchoides besseyi and the chrysanthemum foliar nematode (CFN), Aphelenchoides ritzemabosi are migratory plant parasitic nematodes that infect the aboveground parts of plants. In this research, Arabidopsis thaliana was infected by RWTN and CFN under indoor aseptic cultivation, and the nematodes caused recognizable symptoms in the leaves. Furthermore, RWTN and CFN completed their life cycles and proliferated. Therefore, A. thaliana was identified as a new host of RWTN and CFN...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27909432/volatile-mediated-effects-predominate-in-paraburkholderia-phytofirmans-growth-promotion-and-salt-stress-tolerance-of-arabidopsis-thaliana
#6
Thomas Ledger, Sandy Rojas, Tania Timmermann, Ignacio Pinedo, María J Poupin, Tatiana Garrido, Pablo Richter, Javier Tamayo, Raúl Donoso
Abiotic stress has a growing impact on plant growth and agricultural activity worldwide. Specific plant growth promoting rhizobacteria have been reported to stimulate growth and tolerance to abiotic stress in plants, and molecular mechanisms like phytohormone synthesis and 1-aminocyclopropane-1-carboxylate deamination are usual candidates proposed to mediate these bacterial effects. Paraburkholderia phytofirmans PsJN is able to promote growth of several plant hosts, and improve their tolerance to chilling, drought and salinity...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27908429/callose-associated-silica-deposition-in-arabidopsis
#7
Thibault Brugiére, Christopher Exley
The mechanism of biological silicification in plants remains to be elucidated. There are strong arguments supporting a role for the plant extracellular matrix and the β-1-3-glucan, callose, has been identified as a possible template for silica deposition in the common horsetail, Equisetum arvense. The model plant Arabidopsis thaliana, which is not known as a silica accumulator, can be engineered to produce mutants in which, following a pathogen-associated molecular pattern challenge, callose production in leaves is either induced (35S:PMR4-GFP) or not (pmr4)...
January 2017: Journal of Trace Elements in Medicine and Biology
https://www.readbyqxmd.com/read/27908242/participation-of-two-carbonic-anhydrases-of-the-alpha-family-in-photosynthetic-reactions-in-arabidopsis-thaliana
#8
E M Zhurikova, L K Ignatova, N N Rudenko, V A Mudrik, D V Vetoshkina, B N Ivanov
The expression of genes of two carbonic anhydrases (CA) belonging to the α-family, α-CA2 and α-CA4 (according to the nomenclature in N. Fabre et al. (2007) Plant Cell Environ., 30, 617-629), was studied in arabidopsis (Arabidopsis thaliana, var. Columbia) leaves. The expression of the At2g28210 gene coding α-CA2 decreased under increase in plant illumination, while the expression of the At4g20990 gene coding α-CA4 increased. Under conditions close to optimal for photosynthesis, in plants with gene At2g28210 knockout, the effective quantum yield of photosystem 2 and the light-induced accumulation of hydrogen peroxide in leaves were lower than in wild type plants, while the coefficient of non-photochemical quenching of leaf chlorophyll a fluorescence and the rate of CO2 assimilation in leaves were higher...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27907832/modeling-of-the-catalytic-core-of-arabidopsis-thaliana-dicer-like-4-protein-and-its-complex-with-double-stranded-rna
#9
Agnieszka Mickiewicz, Joanna Sarzyńska, Maciej Miłostan, Anna Kurzyńska-Kokorniak, Agnieszka Rybarczyk, Piotr Łukasiak, Tadeusz Kuliński, Marek Figlerowicz, Jacek Błażewicz
Plant Dicer-like proteins (DCLs) belong to the Ribonuclease III (RNase III) enzyme family. They are involved in the regulation of gene expression and antiviral defense through RNA interference pathways. A model plant, Arabidopsis thaliana encodes four DCL proteins (AtDCL1-4) that produce different classes of small regulatory RNAs. Our studies focus on AtDCL4 that processes double-stranded RNAs (dsRNAs) into 21 nucleotide trans-acting small interfering RNAs. So far, little is known about the structures of plant DCLs and the complexes they form with dsRNA...
November 17, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27905870/transcriptomic-and-proteomic-approach-to-identify-differentially-expressed-genes-and-proteins-in-arabidopsis-thaliana-mutants-lacking-chloroplastic-1-and-cytosolic-fbpases-reveals-several-levels-of-metabolic-regulation
#10
Mauricio Soto-Suárez, Antonio J Serrato, José A Rojas-González, Rocío Bautista, Mariam Sahrawy
BACKGROUND: During the photosynthesis, two isoforms of the fructose-1,6-bisphosphatase (FBPase), the chloroplastidial (cFBP1) and the cytosolic (cyFBP), catalyse the first irreversible step during the conversion of triose phosphates (TP) to starch or sucrose, respectively. Deficiency in cyFBP and cFBP1 isoforms provokes an imbalance of the starch/sucrose ratio, causing a dramatic effect on plant development when the plastidial enzyme is lacking. RESULTS: We study the correlation between the transcriptome and proteome profile in rosettes and roots when cFBP1 or cyFBP genes are disrupted in Arabidopsis thaliana knock-out mutants...
December 1, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27905394/uvr2-ensures-transgenerational-genome-stability-under-simulated-natural-uv-b-in-arabidopsis-thaliana
#11
Eva-Maria Willing, Thomas Piofczyk, Andreas Albert, J Barbro Winkler, Korbinian Schneeberger, Ales Pecinka
Ground levels of solar UV-B radiation induce DNA damage. Sessile phototrophic organisms such as vascular plants are recurrently exposed to sunlight and require UV-B photoreception, flavonols shielding, direct reversal of pyrimidine dimers and nucleotide excision repair for resistance against UV-B radiation. However, the frequency of UV-B-induced mutations is unknown in plants. Here we quantify the amount and types of mutations in the offspring of Arabidopsis thaliana wild-type and UV-B-hypersensitive mutants exposed to simulated natural UV-B over their entire life cycle...
December 1, 2016: Nature Communications
https://www.readbyqxmd.com/read/27900551/transcriptional-regulation-of-snrnas-and-its-significance-for-plant-development
#12
Misato Ohtani
Small nuclear RNA (snRNA) represents a distinct class of non-coding RNA molecules. As these molecules have fundamental roles in RNA metabolism, including pre-mRNA splicing and ribosomal RNA processing, it is essential that their transcription be tightly regulated in eukaryotic cells. The genome of each organism contains hundreds of snRNA genes. Although the structures of these genes are highly diverse among organisms, the trans-acting factors that regulate snRNA transcription are evolutionarily conserved. Recent studies of the Arabidopsis thaliana srd2-1 mutant, which is defective in the snRNA transcription factor, provide insight into the physiological significance of snRNA regulation in plant development...
November 29, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27900506/arabidopsis-thaliana-methionine-sulfoxide-reductase-b8-influences-stress-induced-cell-death-and-effector-triggered-immunity
#13
Shweta Roy, Ashis Kumar Nandi
Reactive oxygen species (ROS) oxidize methionine to methionine sulfoxide (MetSO) and thereby inactivate proteins. Methionine sulfoxide reductase (MSR) enzyme converts MetSO back to the reduced form and thereby detoxifies the effect of ROS. Our results show that Arabidopsis thaliana MSR enzyme coding gene MSRB8 is required for effector-triggered immunity and containment of stress-induced cell death in Arabidopsis. Plants activate pattern-triggered immunity (PTI), a basal defense, upon recognition of evolutionary conserved molecular patterns present in the pathogens...
November 29, 2016: Plant Molecular Biology
https://www.readbyqxmd.com/read/27900439/non-ribosomal-peptide-synthases-from-pseudomonas-aeruginosa-play-a-role-in-cyclodipeptide-biosynthesis-quorum-sensing-regulation-and-root-development-in-a-plant-host
#14
Omar González, Randy Ortíz-Castro, César Díaz-Pérez, Alma L Díaz-Pérez, Viridiana Magaña-Dueñas, José López-Bucio, Jesús Campos-García
Diverse molecules mediate cross-kingdom communication between bacteria and their eukaryotic partners and determine pathogenic or symbiotic relationships. N-acyl-L-homoserine lactone-dependent quorum-sensing signaling represses the biosynthesis of bacterial cyclodipeptides (CDPs) that act as auxin signal mimics in the host plant Arabidopsis thaliana. In this work, we performed bioinformatics, biochemical, and plant growth analyses to identify non-ribosomal peptide synthase (NRPS) proteins of Pseudomonas aeruginosa, which are involved in CDP synthesis...
November 30, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27899679/atpid-a-genome-scale-resource-for-genotype-phenotype-associations-in-arabidopsis
#15
Qi Lv, Yiheng Lan, Yan Shi, Huan Wang, Xia Pan, Peng Li, Tieliu Shi
AtPID (Arabidopsis thaliana Protein Interactome Database, available at http://www.megabionet.org/atpid) is an integrated database resource for protein interaction network and functional annotation. In the past few years, we collected 5564 mutants with significant morphological alterations and manually curated them to 167 plant ontology (PO) morphology categories. These single/multiple-gene mutants were indexed and linked to 3919 genes. After integrated these genotype-phenotype associations with the comprehensive protein interaction network in AtPID, we developed a Naïve Bayes method and predicted 4457 novel high confidence gene-PO pairs with 1369 genes as the complement...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899576/the-nuclear-and-organellar-trna-derived-rna-fragment-population-in-arabidopsis-thaliana-is-highly-dynamic
#16
Valérie Cognat, Geoffrey Morelle, Cyrille Megel, Stéphanie Lalande, Jean Molinier, Timothée Vincent, Ian Small, Anne-Marie Duchêne, Laurence Maréchal-Drouard
In the expanding repertoire of small noncoding RNAs (ncRNAs), tRNA-derived RNA fragments (tRFs) have been identified in all domains of life. Their existence in plants has been already proven but no detailed analysis has been performed. Here, short tRFs of 19-26 nucleotides were retrieved from Arabidopsis thaliana small RNA libraries obtained from various tissues, plants submitted to abiotic stress or fractions immunoprecipitated with ARGONAUTE 1 (AGO1). Large differences in the tRF populations of each extract were observed...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899502/bacillus-subtilis-early-colonization-of-arabidopsis-thaliana-roots-involves-multiple-chemotaxis-receptors
#17
Rosalie Allard-Massicotte, Laurence Tessier, Frédéric Lécuyer, Venkatachalam Lakshmanan, Jean-François Lucier, Daniel Garneau, Larissa Caudwell, Hera Vlamakis, Harsh P Bais, Pascale B Beauregard
: Colonization of plant roots by Bacillus subtilis is mutually beneficial to plants and bacteria. Plants can secrete up to 30% of their fixed carbon via root exudates, thereby feeding the bacteria, and in return the associated B. subtilis bacteria provide the plant with many growth-promoting traits. Formation of a biofilm on the root by matrix-producing B. subtilis is a well-established requirement for long-term colonization. However, we observed that cells start forming a biofilm only several hours after motile cells first settle on the plant...
November 29, 2016: MBio
https://www.readbyqxmd.com/read/27898079/a-dna-element-that-remembers-winter
#18
Chenlong Li, Yuhai Cui
Polycomb-mediated silencing of the floral repressor gene FLC in response to long-term cold is a central event during vernalization in Arabidopsis thaliana, but how it is initiated is unclear. Two new studies identify a DNA element that mediates FLC silencing by attracting a pair of transcriptional repressors, VAL1 and VAL2, which in turn trigger epigenetic silencing by the Polycomb complex PHD-PRC2.
November 29, 2016: Nature Genetics
https://www.readbyqxmd.com/read/27896439/characterization-of-pollen-expressed-bzip-protein-interactions-and-the-role-of-atbzip18-in-the-male-gametophyte
#19
Antónia Gibalová, Lenka Steinbachová, Said Hafidh, Veronika Bláhová, Zuzana Gadiou, Christos Michailidis, Karel Műller, Roman Pleskot, Nikoleta Dupľáková, David Honys
KEY MESSAGE : bZIP TF network in pollen. Transcriptional control of gene expression represents an important mechanism guiding organisms through developmental processes and providing plasticity towards environmental stimuli. Because of their sessile nature, plants require effective gene regulation for rapid response to variation in environmental and developmental conditions. Transcription factors (TFs) provide such control ensuring correct gene expression in spatial and temporal manner. Our work reports the interaction network of six bZIP TFs expressed in Arabidopsis thaliana pollen and highlights the potential functional role for AtbZIP18 in pollen...
November 28, 2016: Plant Reproduction
https://www.readbyqxmd.com/read/27895701/a-dna-based-real-time-pcr-assay-for-robust-growth-quantification-of-the-bacterial-pathogen-pseudomonas-syringae-on-arabidopsis-thaliana
#20
Annegret Ross, Imre E Somssich
BACKGROUND: The interaction of Pseudomonas syringae with Arabidopsis is one of the most commonly used systems to study various bacterial-host interrelationships. Currently, most studies are based on the growth quantification of the pathogen to characterize resistance or virulence targets. However, the standard available method for determining bacterial proliferation in planta is laborious and has several limitations. RESULTS: Here we present an alternative robust approach, which is based on the quantification of bacterial DNA by real-time PCR...
2016: Plant Methods
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