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Plant Journal: for Cell and Molecular Biology

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https://www.readbyqxmd.com/read/28231383/the-pangenome-of-hexaploid-bread-wheat
#1
Juan D Montenegro, Agnieszka A Golicz, Philipp E Bayer, Bhavna Hurgobin, HueyTyng Lee, Chon-Kit Kenneth Chan, Paul Visendi, Kaitao Lai, Jaroslav Doležel, Jacqueline Batley, David Edwards
There is an increasing understanding that gene presence absence variation plays an important role in the heritability of agronomic traits, however there have been relatively few studies on gene presence absence variation in crop species. Hexaploid wheat is one of the most important food crops in the world and intensive breeding has reduced the genetic diversity of elite cultivars. Major efforts have produced draft genome assemblies for the cultivar Chinese Spring, but it is unknown how well this represents the genome diversity found in current modern elite cultivars...
February 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28231382/accurate-measurement-of-transgene-copy-number-in-crop-plants-using-droplet-digital-pcr
#2
Ray Collier, Kasturi Dasgupta, Yan-Ping Xing, Bryan Tarape Hernandez, Min Shao, Dominica Rohozinski, Emma Kovak, Jeanie Lin, Maria Luiza P de Oliveira, Ed Stover, Kent F McCue, Frank G Harmon, Ann Blechl, James G Thomson, Roger Thilmony
Genetic transformation is a powerful means for the improvement of crop plants, but requires labor and resource intensive methods. An efficient method for identifying single copy transgene insertion events from a population of independent transgenic lines is desirable. Currently transgene copy number is estimated by either Southern blot hybridization analyses or quantitative polymerase chain reaction (qPCR) experiments. Southern hybridization is a convincing and reliable method, but it also is expensive, time-consuming and often requires a large amount of genomic DNA and radioactively labeled probes...
February 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28229491/osnla1-a-ring-type-ubiquitin-ligase-maintains-phosphate-homeostasis-in-oryza-sativa-via-degradation-of-phosphate-transporters
#3
Wenhao Yue, Yinghui Ying, Chuang Wang, Yang Zhao, Changhe Dong, James Whelan, Huixia Shou
Inorganic phosphate (Pi) transporters (PTs) play vital roles in Pi uptake and translocation in plants. Under Pi sufficient conditions, PTs are degraded to prevent excess Pi accumulation. The mechanisms targeting PTs for degradation are not fully elucidated. In this study, we found that the Oryza sativa (rice) ortholog of Arabidopsis thaliana Nitrogen Limitation Adaptation (NLA), OsNLA1 protein, a RING-type E3 ubiquitin-ligase, was predominantly localized in the plasma membrane, and could interact with rice phosphate transporters OsPT2 and OsPT8...
February 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28222234/transcriptome-analysis-of-the-brassica-napus-leptosphaeria-maculans-pathosystem-identifies-receptor-signalling-and-structural-genes-underlying-plant-resistance
#4
Michael G Becker, Xuehua Zhang, Philip L Walker, Joey C Wan, Jenna L Millar, Deirdre Khan, Matthew J Granger, Jacob D Cavers, Ainsley C Chan, Dilantha W G Fernando, Mark F Belmonte
The hemibiotrophic fungal pathogen Leptosphaeria maculans is the causal agent of blackleg disease in Brassica napus (canola, oilseed rape) and causes significant yield loss worldwide. While genetic resistance has been used to mitigate the disease using traditional breeding strategies, there is little knowledge about the genes contributing to blackleg resistance. RNA sequencing and a streamlined bioinformatics pipeline identified unique genes and plant defense pathways specific to plant resistance in the B. napus-L...
February 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28218997/wox14-promotes-bioactive-gibberellin-synthesis-and-vascular-cell-differentiation-in-arabidopsis
#5
Erwan Denis, Nadia Kbiri, Viviane Mary, Gaëlle Claisse, Natalia Conde E Silva, Martin Kreis, Yves Deveaux
Procambial and cambial stem cells provide the initial cells that allow the formation of vascular tissues. WOX4 and WOX14 have been shown to act redundantly to promote procambial cell proliferation and differentiation. Gibberellins (GAs), which have an important role in wood formation, also stimulate cambial cell division. Here we show that loss of WOX14 function phenocopies some traits of GA-deficient mutants that can be complemented by exogenous GA application, whereas WOX14 overexpression stimulates the expression of GA3ox anabolism genes and represses GA2ox catabolism genes, promoting the accumulation of bioactive GA...
February 20, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28218992/differently-localized-lysophosphatidic-acid-acyltransferases-crucial-for-triacylglycerol-biosynthesis-in-the-oleaginous-alga-nannochloropsis
#6
Takashi Nobusawa, Koichi Hori, Hiroshi Mori, Ken Kurokawa, Hiroyuki Ohta
Production of renewable bioenergy will be necessary to meet rising global fossil fuel demands. Members of the marine microalgae genus Nannochloropsis produce large amounts of oils (triacylglycerols; TAGs), and this genus is regarded as one of the most promising for biodiesel production. Recent genome sequencing and transcriptomic studies on Nannochloropsis have provided a foundation for understanding its oleaginous trait, but the mechanism underlying oil accumulation remains to be clarified. Here we report Nannochloropsis knockout strains of four extraplastidic lysophosphatidic acid acyltransferases (LPAT1-4), which catalyze a major de novo biosynthetic step of TAGs and membrane lipids...
February 20, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28214361/identification-of-arabidopsis-genic-and-non-genic-promoters-by-paired-end-sequencing-of-tss-tags
#7
Mutsutomo Tokizawa, Kazutaka Kusunoki, Hiroyuki Koyama, Atsushi Kurotani, Tetsuya Sakurai, Yutaka Suzuki, Tomoaki Sakamoto, Tetsuya Kurata, Yoshiharu Y Yamamoto
Information about transcription start sites (TSSs) provides foundational data for analyses of promoter architecture. In this report, we used paired- and single-end deep sequencing to analyze Arabidopsis TSS tags from several libraries prepared from roots, shoots, flowers, and etiolated seedlings. The clustering of approximately 33 million mapped TSS tags led to the identification of 324,461 promoters that covered 79.7% (21,672/27,206) of protein-coding genes in the Arabidopsis genome. In addition, we identified intragenic, antisense, and Orphan promoters that were not associated with any gene models...
February 18, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28207974/aamyb1-and-its-orthologue-atmyb61-affect-terpene-metabolism-and-trichome-development-in-artemisia-annua-and-arabidopsis-thaliana
#8
Luis Matías-Hernández, Weimin Jiang, Ke Yang, Kexuan Tang, Peter E Brodelius, Soraya Pelaz
The effective anti-malarial drug artemisinin (AN) isolated from Artemisia annua is relatively expensive due to the low content in the plant as it is only synthesized within the glandular trichomes. Therefore, genetic engineering of A. annua is one of the most promising approaches to improve AN yield. In this work, AaMYB1 transcription factor has been identified and characterized. When AaMYB1 is overexpressed in A. annua, either exclusively in trichomes or in the whole plant, essential AN biosynthetic genes are also overexpressed and consequently AN amount significantly increased...
February 16, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28207970/molecular-characterization-of-the-c-glucosylation-for-puerarin-biosynthesis-in-pueraria-lobata
#9
Xin Wang, Changfu Li, Chen Zhou, Jia Li, Yansheng Zhang
C-glycosyltransferases (CGTs) are important enzymes that are responsible for the synthesis of the C-glycosides of flavonoids and isoflavonoids. Flavonoid CGTs have been molecularly characterized from several plant species; however, to date, no gene encoding an isoflavonoid CGT has been reported from any plant species. A significant example of an isoflavonoid C-glycoside is puerarin, a compound that contributes to the major medicinal effects of Pueraria lobata. Knowledge regarding the C-glucosylation that occurs during puerarin biosynthesis remains scant...
February 16, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28207953/sgs1-a-neomorphic-nac52-allele-impairing-ptgs-through-sgs3-down-regulation
#10
Nicolas Butel, Ivan Le Masson, Nathalie Bouteiller, Hervé Vaucheret, Taline Elmayan
Post-transcriptional gene silencing (PTGS) is a defense mechanism that targets invading nucleic acids from endogenous (transposons) or exogenous (pathogens, transgenes) origins. Genetic screens based on the reactivation of silenced transgenes have long been used to identify cellular PTGS components and regulators. Here we show that the first isolated PTGS-deficient mutant, sgs1, is impaired in the transcription factor NAC52. This mutant exhibits striking similarities with a mutant impaired in the H3K4me3 demethylase JMJ14 isolated from the same genetic screen...
February 16, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28182317/impact-of-light-intensity-and-quality-on-chromatophore-and-nuclear-gene-expression-in-paulinella-chromatophora-an-amoeba-with-nascent-photosynthetic-organelles
#11
Ru Zhang, Eva C M Nowack, Dana C Price, Debashish Bhattacharya, Arthur R Grossman
Plastid evolution has been attributed to a single primary endosymbiotic event that occurred ~1.6 BYA in which a cyanobacterium was engulfed and retained by a eukaryotic cell, although early steps in plastid integration are poorly understood. The photosynthetic amoeba Paulinella chromatophora represents a unique model to study plastid evolution because it contains cyanobacterium-derived photosynthetic organelles termed "chromatophores" that originated relatively recently (0.06-0.14 BYA). The chromatophore genome is ~1/3 the size of the genome of closely related cyanobacteria, but 10-fold larger than most plastid genomes...
February 9, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28182313/h3k23me1-is-an-evolutionary-conserved-histone-modification-associated-with-cg-dna-methylation-in-arabidopsis
#12
Minerva S Trejo-Arellano, Walid Mahrez, Miyuki Nakamura, Jordi Moreno-Romero, Paolo Nanni, Claudia Köhler, Lars Hennig
Amino-terminal tails of histones are targets for diverse post-translational modifications whose combinatorial action may constitute a code that will be read and interpreted by cellular proteins to define particular transcriptional states. Here, we describe monomethylation of histone H3 lysine 23 (H3K23me1) as a histone modification not previously described in plants. H3K23me1 is an evolutionary conserved mark in diverse flowering plant species. Chromatin immunoprecipitation followed by high-throughput sequencing in Arabidopsis thaliana showed that H3K23me1 was highly enriched in pericentromeric regions and depleted from chromosome arms...
February 9, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28181322/leunig_homolog-transcriptional-co-repressor-mediates-aluminum-sensitivity-through-pectin-methylesterase46-modulated-root-cell-wall-pectin-methylesterification-in-arabidopsis
#13
Xiaoyu Geng, Walter J Horst, John F Golz, Joanne E Lee, Zhaojun Ding, Zhong-Bao Yang
A major factor determining aluminum (Al) sensitivity in higher plants is the binding of Al to root cell walls. The Al binding capacity of cell walls is closely linked to the extent of pectin methylesterification, as presence of methyl groups attached to the pectin backbone reduces the net negative charge of this polymer and hence limits Al binding. Despite recent progress in understanding the molecular basis of Al resistance in a wide range of plants, it is not well understood how the methylation status of pectin is mediated in response to Al stress...
February 9, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28161906/sexual-reproduction-sporophyte-development-and-molecular-variation-in-the-model-moss-physcomitrella-patens-introducing-the-ecotype-reute
#14
Manuel Hiss, Rabea Meyberg, Jens Westermann, Fabian B Haas, Lucas Schneider, Mareike Schallenberg-Rüdinger, Kristian K Ullrich, Stefan A Rensing
Rich ecotype collections are used for several plant models to unravel the molecular causes of phenotypic differences and to investigate effects of environmental adaption and acclimation. For the model moss Physcomitrella patens, collections of accessions are available and have been used e.g. for phylogenetic and taxonomic studies, but few have been investigated further for phenotypic differences. Here, we focus on the Reute accession and provide expression profiling and comparative developmental data for several stages of sporophyte development, as well as information on genetic variation via genomic sequencing...
February 5, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28161903/phosphatidic-acid-binding-inhibits-rgs1-activity-to-affect-specific-signaling-pathways-in-arabidopsis
#15
Swarup Roy Choudhury, Sona Pandey
Modulation of the active versus inactive forms of the Gα protein is critical for the signaling processes mediated by the heterotrimeric G-protein complex. We have recently established that in Arabidopsis, the regulator of G-protein signaling (RGS1) protein and a lipid hydrolyzing enzyme, phospholipase Dα1 (PLDα1), both act as GTPase-activity accelerating proteins (GAP) for the Gα protein to attenuate its activity. RGS1 and PLDα1 interact with each other and RGS1 inhibits the activity of PLDα1 during regulation of a subset of responses...
February 5, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28161902/phylogenomic-analysis-of-gene-co-expression-networks-reveals-the-evolution-of-functional-modules
#16
Colin Ruprecht, Sebastian Proost, Marcela Hernandez-Coronado, Carlos Ortiz-Ramirez, Daniel Lang, Stefan A Rensing, Jörg D Becker, Klaas Vandepoele, Marek Mutwil
Molecular evolutionary studies correlate genomic and phylogenetic information with the emergence of new traits of organisms. These traits are, however, the consequence of dynamic gene networks composed of functional modules, which might not be captured by genomic analyses. Here, we established a method, which combines large-scale genomic and phylogenetic data with gene co-expression networks, to extensively study the evolutionary make-up of modules in the moss Physcomitrella patens and in the angiosperms Arabidopsis thaliana and rice...
February 5, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28161901/shoot-meristemless-trafficking-controls-axillary-meristem-formation-meristem-size-and-organ-boundaries-in-arabidopsis
#17
Rachappa Balkunde, Munenori Kitagawa, Xianfeng Morgan Xu, Jing Wang, David Jackson
The shoot stem cell niche, contained within the shoot apical meristem (SAM) is maintained in Arabidopsis by the homeodomain protein SHOOT MERISTEMLESS (STM). STM is a mobile protein that traffics cell-to-cell, presumably through plasmodesmata. In maize, the STM homolog KNOTTED1 shows clear differences between mRNA and protein localization domains in the SAM. However, the STM mRNA and protein localization domains are not obviously different in Arabidopsis, and the functional relevance of STM mobility is unknown...
February 5, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28161893/identification-and-characterization-of-a-stable-intermediate-in-photosystem-i-assembly-in-tobacco
#18
Gal Wittenberg, Sari Järvi, Marta Hojka, Szilvia Z Tóth, Etienne H Meyer, Eva-Mari Aro, Mark Aurel Schöttler, Ralph Bock
PSI is the most efficient bioenergetic nanomachine in nature and one of the largest membrane protein complexes known. It is composed of 18 protein subunits that bind more than 200 co-factors and prosthetic groups. While the structure and function of PSI have been studied in great detail, very little is known about the PSI assembly process. In this work, we have characterized a PSI assembly intermediate in tobacco plants, which we named PSI*. We found PSI* to contain only a specific subset of the core subunits of PSI...
February 5, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28155248/mutants-in-the-imprinted-pickle-related-2-gene-suppress-seed-abortion-of-fertilization-independent-seed-class-mutants-and-paternal-excess-interploidy-crosses-in-arabidopsis
#19
Fang Huang, Qian-Hao Zhu, Anyu Zhu, Xiaoba Wu, Liqiong Xie, Xianjun Wu, Chris Helliwell, Abed Chaudhury, E Jean Finnegan, Ming Luo
Endosperm cellularization is essential for embryo development and viable seed formation. Loss of function of the FERTILIZATION INDEPENDENT SEED (FIS) class Polycomb genes, which mediate histone H3 lysine27 trimethylation (H3K27me3), as well as imbalanced contributions of parental genomes interrupt this process. What causes the failure of cellularization is poorly understood. In this study, we identified PICKLE RELATED 2 (PKR2), mutations which suppress seed abortion in fis1/mea by restoring endosperm cellularization...
February 3, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28155243/rad54-forms-dna-repair-foci-in-response-to-dna-damage-in-living-plant-cells
#20
Takeshi Hirakawa, Junko Hasegawa, Charles I White, Sachihiro Matsunaga
Plants have various defense mechanisms against environmental stresses that induce DNA damage. Genetic and biochemical analyses have revealed the sensing and signaling of DNA damage, but little is known about the subnuclear dynamics in response to DNA damage in living plant cells. Here, we observed that the chromatin remodeling factor RAD54, which is involved in DNA repair via the homologous recombination pathway, formed subnuclear foci (termed RAD54 foci) in Arabidopsis thaliana after DNA double-strand break induction...
February 2, 2017: Plant Journal: for Cell and Molecular Biology
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