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https://www.readbyqxmd.com/read/29353158/quantification-of-light-induced-minisog-superoxide-production-using-the-selective-marker-2-hydroxyethidium
#1
Miriam E Barnett, Timothy M Baran, Thomas H Foster, Andrew P Wojtovich
Genetically-encoded photosensitizers produce reactive oxygen species (ROS) in response to light. Transgenic expression of fusion proteins can target the photosensitizers to specific cell regions and permit the spatial and temporal control of ROS production. These ROS-generating proteins (RGPs) are widely used for cell ablation, mutagenesis and chromophore-assisted light inactivation of target proteins. However, the species produced by RGPs are unclear due to indirect measures with confounding interpretations...
January 17, 2018: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/29352810/ectopic-expression-of-the-apple-nucleus-encoded-thylakoid-protein-mdy3ip1-triggers-early-flowering-and-enhanced-salt-tolerance-in-arabidopsis-thaliana
#2
Jian-Qiang Yu, Jia-Hui Wang, Cui-Hui Sun, Quan-Yan Zhang, Da-Gang Hu, Yu-Jin Hao
BACKGROUND: The roles in photosystem I (PSI) assembly of the nucleus-encoded thylakoid protein Y3IP1 who interacts with the plastid-encoded Ycf3 protein that has been well-characterized in plants. However, its function and potential mechanisms in other aspects remain poorly understood. RESULTS: We identified the apple MdY3IP1 gene, which encodes a protein highly homologous to the Arabidopsis Y3IP1 (AtY3IP1). Ectopic expression of MdY3IP1 triggered early-flowering and enhanced salt tolerance in Arabidopsis plants...
January 20, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29352746/the-common-bean-cok-4-and-the-arabidopsis-fer-kinase-domain-share-similar-function-in-plant-growth-and-defense
#3
Rafhael Felipin Azevedo, Maria Celeste Gonçalves Vidigal, Paula Rodrigues Oblessuc, Maeli Melotto
Receptor-like kinases are membrane proteins that can be shared by diverse signaling pathways. Among them, the Arabidopsis thaliana FERONIA (FER) plays a role in the balance between distinct signals to control growth and defense. We have found that COK-4, a putative kinase encoded in the common bean anthracnose resistance locus Co-4 that is transcriptionally regulated during immune response, is highly similar to the kinase domain of FER. To assess whether COK-4 is a functional ortholog of FER, we expressed COK-4 in the wild type Col-0 and the fer-5 mutant of Arabidopsis and evaluated FER-associated traits...
January 20, 2018: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29352229/expression-dynamics-of-mirnas-and-their-targets-in-seed-germination-conditions-reveals-mirna-ta-sirna-crosstalk-as-regulator-of-seed-germination
#4
Shabari Sarkar Das, Sandeep Yadav, Archita Singh, Vibhav Gautam, Ananda K Sarkar, Asis K Nandi, Prakash Karmakar, Manoj Majee, Neeti Sanan-Mishra
Seed germination paves the way for the dormant embryo to establish itself as a new plant marking the first critical step in postembryonic plant growth and development. Germination starts with the uptake of water (imbibition), followed by induction of transcription, translation, energy metabolism, and cell division processes. Although small RNAs have been implicated in many developmental processes, their role during seed germination stages and conditions remained elusive. Here we show that seed germination conditions, like imbibition and temperature, dynamically regulate the expression of many developmentally important miRNAs and their targets...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352064/gif-transcriptional-co-regulators-control-root-meristem-homeostasis
#5
María Florencia Ercoli, Antonella Ferela, Juan M Debernardi, Ana Paula Perrone, Ramiro E Rodriguez, Javier Fernando Palatnik
In the root meristem, the quiescent center (QC) is surrounded by stem cells, which in turn generate the different cell types of the root. QC cells rarely divide under normal conditions but can replenish damaged stem cells. In the proximal meristem, the daughters of stem cells, which are referred to as transit amplifying cells, undergo additional rounds of cell division prior to differentiation. Here, we describe the functions of GRF-INTERACTING FACTORs (GIFs), including ANGUSTIFOLIA3 (AN3), in Arabidopsis thaliana roots...
January 18, 2018: Plant Cell
https://www.readbyqxmd.com/read/29352063/arabidopsis-thaliana-fancd2-promotes-meiotic-crossover-formation
#6
Marie-Therese Kurzbauer, Monica Pradillo, Claudia Kerzendorfer, Jason Sims, Rene Ladurner, Cecilia Oliver, Michael Peter Janisiw, Magdalena Mosiolek, Dieter Schweizer, Gregory P Copenhaver, Peter Schlogelhofer
Fanconi anemia (FA) is a human autosomal recessive disorder characterized by chromosomal instability, developmental pathologies, predisposition to cancer and reduced fertility. So far, nineteen genes have been implicated in FA, most of them involved in DNA repair. Some are conserved across higher eukaryotes, including plants. The Arabidopsis thaliana genome encodes a homologue of the Fanconi anemia D2 gene (FANCD2) whose function in DNA repair is not yet fully understood. Here we provide evidence that AtFANCD2 is required for meiotic homologous recombination...
January 19, 2018: Plant Cell
https://www.readbyqxmd.com/read/29350358/streptomyces-ach-505-triggers-production-of-a-salicylic-acid-analogue-in-the-fungal-pathogen-heterobasidion-abietinum-that-enhances-infection-of-norway-spruce-seedlings
#7
Nadine Keilhofer, Jonny Nachtigall, Andreas Kulik, Margret Ecke, Rüdiger Hampp, Roderich D Süssmuth, Hans-Peter Fiedler, Silvia D Schrey
The necrotrophic fungus Heterobasidion spp. is the causal agent of 'annosum root rot' of Norway spruce. In the presence of the rhizosphere bacterium Streptomyces AcH 505, enhanced colonization of Norway spruce roots with Heterobasidion abietinum 331 has previously been observed. By analyzing dual cultures of H. abietinum 331 and Streptomyces AcH 505 with HPLC, a fungal metabolite was identified that was increased in the presence of Streptomyces AcH 505. Likewise, challenge of H. abietum 331 with common antifungals produced by soil streptomycetes rendered the same effect...
January 19, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29348608/phytase-overexpression-in-arabidopsis-improves-plant-growth-under-osmotic-stress-and-in-combination-with-phosphate-deficiency
#8
Nibras Belgaroui, Benoit Lacombe, Hatem Rouached, Moez Hanin
Engineering osmotolerant plants is a challenge for modern agriculture. An interaction between osmotic stress response and phosphate homeostasis has been reported in plants, but the identity of molecules involved in this interaction remains unknown. In this study we assessed the role of phytic acid (PA) in response to osmotic stress and/or phosphate deficiency in Arabidopsis thaliana. For this purpose, we used Arabidopsis lines (L7 and L9) expressing a bacterial beta-propeller phytase PHY-US417, and a mutant in inositol polyphosphate kinase 1 gene (ipk1-1), which were characterized by low PA content, 40% (L7 and L9) and 83% (ipk1-1) of the wild-type (WT) plants level...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348240/snf1-related-kinase1-controlled-c-s1-bzip-signaling-activates-alternative-mitochondrial-metabolic-pathways-to-ensure-plant-survival-in-extended-darkness
#9
Lorenzo Pedrotti, Christoph Weiste, Thomas Nägele, Elmar Wolf, Francesca Lorenzin, Katrin Dietrich, Andrea Mair, Wolfram Weckwerth, Markus Teige, Elena Baena-González, Wolfgang Dröge-Laser
Sustaining energy homeostasis is of pivotal importance for all living organisms. In Arabidopsis thaliana, evolutionarily conserved SnRK1 kinases (Snf1-RELATED KINASE1) control metabolic adaptation during low energy stress. To unravel starvation-induced transcriptional mechanisms, we performed transcriptome studies of inducible knock-down lines and found that S1-basic leucine Zipper transcription factors (S1-bZIPs) control a defined subset of genes downstream of SnRK1. For example, S1-bZIPs coordinate the expression of genes involved in branched-chain amino acid catabolism, which constitutes an alternative mitochondrial respiratory pathway that is crucial for plant survival during starvation...
January 18, 2018: Plant Cell
https://www.readbyqxmd.com/read/29343504/canonical-and-non-canonical-actions-of-arabidopsis-histone-deacetylases-in-ribosomal-rna-processing
#10
Xiangsong Chen, Li Lu, Shuiming Qian, Mark Scalf, Lloyd M Smith, Xuehua Zhong
Ribosome biogenesis is a fundamental process required for all cellular activities. Histone deacetylases play critical roles in many biological processes including transcriptional repression and rDNA silencing. However, their function in pre-rRNA processing remains poorly understood. Here, we discovered a previously uncharacterized role of Arabidopsis thaliana histone deacetylase HD2C in pre-rRNA processing via both canonical and non-canonical manners. HD2C interacts with another histone deacetylase HD2B and forms homo- and/or hetero-oligomers in the nucleolus...
January 17, 2018: Plant Cell
https://www.readbyqxmd.com/read/29343218/loctext-relation-extraction-of-protein-localizations-to-assist-database-curation
#11
Juan Miguel Cejuela, Shrikant Vinchurkar, Tatyana Goldberg, Madhukar Sollepura Prabhu Shankar, Ashish Baghudana, Aleksandar Bojchevski, Carsten Uhlig, André Ofner, Pandu Raharja-Liu, Lars Juhl Jensen, Burkhard Rost
BACKGROUND: The subcellular localization of a protein is an important aspect of its function. However, the experimental annotation of locations is not even complete for well-studied model organisms. Text mining might aid database curators to add experimental annotations from the scientific literature. Existing extraction methods have difficulties to distinguish relationships between proteins and cellular locations co-mentioned in the same sentence. RESULTS: LocText was created as a new method to extract protein locations from abstracts and full texts...
January 17, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29342073/structure-elucidation-of-unknown-metabolites-in-metabolomics-by-combined-nmr-and-ms-ms-prediction
#12
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/29341143/loss-of-alkaline-ceramidase-inhibits-autophagy-in-arabidopsis-and-plays-an-important-role-during-environmental-stress-response
#13
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
#14
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
#15
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
#16
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/29339437/spr2-protects-minus-ends-to-promote-severing-and-reorientation-of-plant-cortical-microtubule-arrays
#17
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/29337078/circadian-waves-of-transcriptional-repression-shape-pif-regulated-photoperiod-responsive-growth-in-arabidopsis
#18
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
#19
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
#20
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
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