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Plant Journal: for Cell and Molecular Biology

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https://www.readbyqxmd.com/read/30604905/cytonuclear-interactions-remain-stable-during-allopolyploid-evolution-despite-repeated-whole-genome-duplications-in-brassica
#1
Julie Ferreira de Carvalho, Jérémy Lucas, Gwenaëlle Deniot, Cyril Falentin, Olivier Filangi, Marie Gilet, Fabrice Legeai, Maryse Lode, Jérôme Morice, Gwenn Trotoux, Jean-Marc Aury, Valérie Barbe, Jean Keller, Rod Snowdon, Zhesi He, France Denoeud, Patrick Wincker, Ian Bancroft, Anne-Marie Chèvre, Mathieu Rousseau-Gueutin
Several plastid macromolecular protein complexes are encoded by both nuclear and plastid genes. Therefore, cytonuclear interactions are held in place to prevent genomic conflicts that may lead to incompatibilities. Allopolyploidy resulting from hybridization and genome doubling of two divergent species, can disrupt these fine-tuned interactions, as newly formed allopolyploid species confront biparental nuclear chromosomes with uniparentally inherited plastid genome. To avoid any deleterious effects of unequal genome inheritance, preferential transcription of the plastid donor over the other one has been hypothesized to occur in allopolyploids...
January 3, 2019: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30604574/suppression-of-tryptophan-synthase-activates-cotton-immunity-by-triggering-cell-death-via-promoting-sa-synthesis
#2
Yuhuan Miao, Lian Xu, Xin He, Lin Zhang, Muhammad Shaban, Xianlong Zhang, Longfu Zhu
Primary metabolism plays important roles in plant growth and development. However, the relationship between primary metabolism and adaptive immune response is largely unknown. Here, we employed RNA interference (RNAi), virus induced gene silencing (VIGS) technology, phytohormone profiling, genetic studies, and transcriptome and metabolome analysis to investigate the function of the tryptophan synthesis pathway in the resistance of cotton to V. dahliae. We find that knock-down of GbTSA1 (Tryptophan Synthase α) and GbTSB1 (Tryptophan Synthase β) induces a spontaneous cell death phenotype in a SA-dependent manner and enhanced resistance to V...
January 3, 2019: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30604453/enhancing-microrna167a-expression-in-seed-decreases-the-%C3%AE-linolenic-acid-content-and-increases-seed-size-in-camelina-sativa
#3
GunNam Na, Xiaopeng Mu, Paul Grabowski, Jeremy Schmutz, Chaofu Lu
Despite well-established roles of microRNAs in plant development, little has been addressed to understand their effects in seeds especially on lipid metabolism. In this study, we showed that overexpressing microRNA167A (miR167OE) in camelina (Camelina sativa) under a seed-specific promoter changed fatty acid composition and increased seed size. Specifically, the miR167OE seeds had a lower α-linolenic acid with a concomitantly higher linoleic acid content than the wild type. This decreased level of fatty acid desaturation corresponded to a decreased transcriptional expression of the camelina fatty acid dsesaturase3 (CsFAD3) in developing seeds...
January 3, 2019: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30604579/mitochondrial-complex-ii-of-plants-subunit-composition-assembly-and-function-in-respiration-and-signaling
#4
Shaobai Huang, Hans-Peter Braun, Ryan M R Gawryluk, A Harvey Millar
Complex II (succinate dehydrogenase [succinate-ubiquinone oxidoreductase]; EC 1.3.5.1; SDH) is the only enzyme shared by both the electron transport chain and the tricarboxylic acid (TCA) cycle in mitochondria. Complex II in plants is considered unusual due to its accessory subunits (SDH5-8) in addition to the catalytic subunits of SDH found in all eukaryotes (SDH1-4). Here we review compositional and phylogenetic analysis, and biochemical dissection studies to clarify the presence and to propose the role of these subunits...
January 2, 2019: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30604489/phloem-loading-in-cucumber-combined-symplastic-and-apoplastic-strategies
#5
Si Ma, Lulu Sun, Xiaolei Sui, Yaxin Li, Ying Chang, Jingwei Fan, Zhenxian Zhang
Phloem loading, as the first step of transporting photoassimilates from mesophyll cells to sieve element-companion cell complex, creates a driving force for long-distance nutrient transport. Three loading strategies have been proposed: passive symplastic loading, apoplastic loading and symplastic transfer followed by polymer-trapping of stachyose and raffinose. Although individual species are generally referred to as using a single phloem loading mechanism, it has been suggested that some plants may use more than one, i...
January 2, 2019: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30604470/high-throughput-3d-modelling-to-dissect-the-genetic-control-of-leaf-elongation-in-barley-hordeum-vulgare
#6
Ben Ward, Chris Brien, Helena Oakey, Allison Pearson, Sónia Negrão, Rhiannon K Schilling, Julian Taylor, David Jarvis, Andy Timmins, Stuart J Roy, Mark Tester, Bettina Berger, Anton van den Hengel
To optimize shoot growth and structure of cereals, we need to understand the genetic components controlling initiation and elongation. While measuring total shoot growth at high-throughput using 2D imaging has progressed, recovering the 3D shoot structure of small grain cereals at a large scale is still challenging. Here, we present a method for measuring defined individual leaves of cereals, such as wheat and barley, using few images. Plant shoot modelling over time was used to measure the initiation and elongation of leaves in a bi-parental barley mapping population under low and high soil salinity...
January 2, 2019: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30604455/arabidopsis-pcap2-modulates-the-phosphatidylinositol-4-5-bisphosphate-signal-on-the-plasma-membrane-and-attenuates-root-hair-elongation
#7
Mariko Kato, Tomohiko Tsuge, Masayoshi Maeshima, Takashi Aoyama
Phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2 ] serves as a subcellular signal on the plasma membrane, mediating various cell-polarized phenomena including polar cell growth. Here, we investigated the involvement of Arabidopsis thaliana PCaP2, a plant-unique plasma membrane protein with phosphoinositide-binding activity, in PtdIns(4,5)P2 signaling for root hair tip growth. The long-root-hair phenotype of the pcap2 knockdown mutant was found to stem from its higher average root hair elongation rate compared with the wild type and to counteract the low average rate caused by a defect in the PtdIns(4,5)P2 -producing enzyme gene PIP5K3...
January 2, 2019: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30589143/rapid-and-reproducible-phosphopeptide-enrichment-by-tandem-moac-application-to-boron-deficiency-induced-phosphoproteomics
#8
Yanmei Chen, Wolfgang Hoehenwarter
Mass spectrometry has been instrumental in enabling the study of molecular signaling on a cellular scale by way of site-specific quantification of protein post translational modifications, in particular phosphorylation. Here we describe an updated tandem MOAC combined phosphoprotein / phosphopeptide enrichment strategy, a scalable phosphoproteomics approach that allows rapid identification of thousands of phophopeptides in plant materials. We implemented modifications to several steps of the original tandem MOAC procedure to increase the amount of quantified phosphopeptides and hence site specific phosphorylation of proteins in a sample beginning with the less amounts of tissue and a substantially smaller amount of extracted protein...
December 27, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30589140/osshoc1-and-osptd1-are-essential-for-crossover-formation-during-rice-meiosis
#9
Yun Ren, Dan Chen, Wenjie Li, Dan Zhou, Tao Luo, Guoqiang Yuan, Jing Zeng, Ye Cao, Zhongshan He, Ting Zou, Qiming Deng, Shiquan Wang, Aiping Zheng, Jun Zhu, Yueyang Liang, Huainian Liu, Lingxia Wang, Ping Li, Shuangcheng Li
Meiosis is essential for eukaryotic sexual reproduction and plant fertility, and crossovers (COs) are essential for meiosis and the formation of new allelic combinations in gametes. In this study, we report the isolation of a meiotic gene, OsSHOC1, and the identification of its partner, OsPTD1. Osshoc1 was sterile both in male and female gametophytes, and it showed a striking reduction in the number of meiotic COs, indicating that OsSHOC1 was required for normal CO formation. Further investigations showed that OsSHOC1 physically interacted with OsPTD1 and that the latter was also required for normal CO formation and plant fertility...
December 27, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30584677/targeted-exome-sequencing-of-unselected-heavy-ion-beam-irradiated-populations-reveals-less-biased-mutation-characteristics-in-the-rice-genome
#10
Hiroyuki Ichida, Ryouhei Morita, Yuki Shirakawa, Yoriko Hayashi, Tomoko Abe
Heavy-ion beams have been widely utilized as a novel and effective mutagen for mutation breeding in diverse plant species, but the induced mutation spectrum is not fully understood at the genome scale. We describe the development of a multiplexed and cost-efficient whole-exome sequencing procedure in rice, and its application to characterize an unselected population of heavy-ion beam-induced mutations. The bioinformatics pipeline identified single-nucleotide mutations as well as small and large (>63 kb) insertions and deletions, and showed good agreement with the results obtained with conventional PCR and sequencing analyses...
December 25, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30577085/srna-fish-versatile-fluorescent-in-situ-detection-of-small-rnas-in-plants
#11
Kun Huang, Patricia Baldrich, Blake C Meyers, Jeffrey L Caplan
Localization of mRNA and small RNAs (sRNA) is important for understanding their function. Fluorescent in situ hybridization (FISH) has been used extensively in animal systems to study sRNA localization and expression. However, current methods for fluorescent in situ detection of sRNA in plant tissues are less developed. Here we report a protocol for sRNA-FISH, for efficient fluorescent detection of sRNAs in plants. sRNA-FISH is suitable for application in diverse plant species and tissue types. The use of Locked Nucleic Acid (LNA) probes and antibodies conjugated with different fluorophores allows the detection of two sRNAs in the same sample...
December 21, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30570818/extreme-variation-in-rates-of-evolution-in-the-plastid-clp-protease-complex
#12
Alissa M Williams, Giulia Friso, Klaas J van Wijk, Daniel B Sloan
Eukaryotic cells represent an intricate collaboration between multiple genomes, even down to the level of multisubunit complexes in mitochondria and plastids. One such complex in plants is the caseinolytic protease (Clp), which plays an essential role in plastid protein turnover. The proteolytic core of Clp comprises subunits from one plastid-encoded gene (clpP1) and multiple nuclear genes. The clpP1 gene is highly conserved across most green plants, but it is by far the fastest evolving plastid-encoded gene in some angiosperms...
December 20, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30570805/differential-alternative-polyadenylation-contributes-to-the-developmental-divergence-between-two-rice-subspecies-japonica-and-indica
#13
Qian Zhou, Haihui Fu, Dewei Yang, Congting Ye, Sheng Zhu, Juncheng Lin, Wenbin Ye, Guoli Ji, Xinfu Ye, Xiaohui Wu, Qingshun Quinn Li
Alternative polyadenylation (APA) is a widespread post-transcriptional mechanism that regulates gene expression through mRNA metabolism, playing a pivotal role in modulating rice (Oryza sativa L.) phenotypic traits. However, little is known about APA-mediated regulations underlying the distinct characteristics between two major rice subspecies, Indica and Japonica. Using poly(A)-tag sequencing approach, polyadenylation (poly(A)) site profiles were investigated and compared pairwise from germinating to mature stage between Indica and Japonica, and extensive differentiation in APA profiles were detected genome-wide...
December 20, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30570804/ice1-and-zou-determine-the-depth-of-primary-seed-dormancy-in-arabidopsis-independently-of-their-role-in-endosperm-development
#14
Dana R MacGregor, Naichao Zhang, Mayumi Iwasaki, Min Chen, Anuja Dave, Luis Lopez-Molina, Steven Penfield
Seed dormancy is a widespread and key adaptive trait that is essential for the establishment of soil seed banks and prevention of preharvest sprouting. Herein we demonstrate that the endosperm-expressed transcription factors ZHOUPI (ZOU) and INDUCER OF CBF EXPRESSION1 (ICE1) play a role in determining primary dormancy depth in Arabidopsis. We show that ice1 or zou increases seed dormancy and the double mutant has an additive phenotype. The increased dormancy is associated with increased ABA levels, and can be separated genetically from their role in endosperm maturation, because loss of ABA biosynthesis or DELAY OF GERMINATION 1 reverses the dormancy phenotype without affecting the aberrant seed morphology...
December 20, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30570803/comparative-analyses-of-ros-producing-enzymatic-activity-of-arabidopsis-nadph-oxidases
#15
Hidetaka Kaya, Seiji Takeda, Masaki J Kobayashi, Sachie Kimura, Ayako Iizuka, Aya Imai, Haruka Hishinuma, Tomoko Kawarazaki, Kyoichiro Mori, Yuta Yamamoto, Yuki Murakami, Ayuko Nakauchi, Mitsutomo Abe, Kazuyuki Kuchitsu
Reactive oxygen species (ROS) produced by NADPH oxidases, respiratory burst oxidase homologs (Rbohs), play crucial roles in development as well as biotic and abiotic stress responses in plants. Arabidopsis has ten Rboh genes, AtRbohA to AtRbohJ. Five AtRbohs (AtRbohC, D, F, H and J) are synergistically activated by Ca2+ and protein phosphorylation to produce ROS that play various roles in planta, although the activities of the other Rbohs remain unknown. With a heterologous expression system, we found a range in ROS-producing activity among the AtRbohs with differences up to 100 times, indicating that the required ROS amount is different in each situation where the AtRbohs act...
December 20, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30570783/lotus-shaggy-like-kinase-1-is-required-to-suppress-nodulation-in-lotus-japonicus
#16
C Garagounis, D Tsikou, P K Plitsi, I S Psarrakou, M Avramidou, C Stedel, M Anagnostou, M E Georgopoulou, K K Papadopoulou
Glycogen Synthase Kinase/Shaggy-like kinases (SKs) are a highly conserved family of signaling proteins that participate in many developmental, cell-differentiation, and metabolic signaling pathways in plants and animals. Here, we investigate the involvement of SKs in legume nodulation, a process requiring integration of multiple signaling pathways. We describe a group of SKs in the model legume Lotus japonicus (LSKs), two of which respond to inoculation with the symbiotic nitrogen-fixing bacterium Mesorhizobium loti...
December 20, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30561788/a-newly-identified-cluster-of-glutathione-s-transferase-genes-provides-verticillium-wilt-resistance-in-cotton
#17
Zhi-Kun Li, Bin Chen, Xiu-Xin Li, Jin-Peng Wang, Yan Zhang, Xing-Fen Wang, Yuan-Yuan Yan, Hui-Feng Ke, Jun Yang, Jin-Hua Wu, Guo-Ning Wang, Gui-Yin Zhang, Li-Qiang Wu, Xi-Yin Wang, Zhi-Ying Ma
As the largest cultivated fiber crop in the world, cotton (Gossypium hirsutum) is often exposed to various biotic stresses during its growth periods. Verticillium wilt, caused by Verticillium dahliae, is a severe disease in cotton, and the molecular mechanism of cotton resistance to Verticillium wilt needs to be further investigated. Here, we revealed that the cotton genome contained nine types of GST genes. An evolutionary analysis showed that a newly-identified cluster (including Gh_A09G1508, Gh_A09G1509 and Gh_A09G1510) located on chromosome 09 of the A-subgenome and was under positive selection pressure during the formation of the allotetraploid...
December 18, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30556936/gene-networks-orchestrated-by-megi-a-single-factor-mechanism-underlying-sex-determination-in-persimmon
#18
Ho-Wen Yang, Takashi Akagi, Taiji Kawakatsu, Ryutaro Tao
Separating male and female sex organs is one of the main strategies used to maintain genetic diversity within a species. However, the genetic determinants and their regulatory mechanisms have been identified in only a few species. In dioecious persimmons, the homeodomain transcription factor, MeGI, which is the target of a Y chromosome-encoded small-RNA, OGI, can determine floral sexuality. The basic features of this system are conserved in the monoecious hexaploid Oriental persimmon, where an additional epigenetic regulation of MeGI determines floral sexuality...
December 17, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30556198/characterization-of-lrl5-as-a-key-regulator-of-root-hair-growth-in-maize
#19
Chun-Xia Wang, Chuang-Ye Qi, Jin-Hong Luo, Lin Liu, Yan He, Li-Qun Chen
Root hair, the special type of tubular-shaped cell, outgrows from root epidermal cell and plays important roles in the acquisition of nutrient and water, as well as the interactions with biotic and abiotic stresses. Studies in the model plant Arabidopsis have revealed that the root-hair initiation and elongation are hierarchically regulated by a group of basic helix-loop-helix (bHLH) transcription factors (TFs). However, knowledge regarding the regulatory pathways of these bHLH-TFs in controlling root hair growth remains limited...
December 17, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30556340/identification-and-characterization-of-a-core-set-of-ros-wave-associated-transcripts-involved-in-the-systemic-acquired-acclimation-response-of-arabidopsis-to-excess-light
#20
Sara I Zandalinas, Soham Sengupta, David Burks, Rajeev K Azad, Ron Mittler
Systemic acquired acclimation (SAA) plays a key role in optimizing growth and preventing damages associated with fluctuating or abrupt changes in the plant environment. To be effective, SAA has to occur at a rapid rate and depend on rapid signaling pathways that transmit signals from affected tissues to all parts of the plant. Although recent studies identified several different rapid systemic signaling pathways that could mediate SAA, very little is known about the extent of their involvement in mediating transcriptomic responses...
December 16, 2018: Plant Journal: for Cell and Molecular Biology
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