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Plant Journal: for Cell and Molecular Biology

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https://www.readbyqxmd.com/read/28333395/small-molecules-belowground-the-role-of-specialized-metabolites-in-the-rhizosphere
#1
Hassan Massalha, Elisa Korenblum, Dorothea Tholl, Asaph Aharoni
Soil communities are diverse taxonomically and functionally. This ecosystem experiences highly complex networks of interactions, but may also present functionally independent entities. Plant roots, a metabolically active hotspot in the soil, take an essential part in belowground interactions. While plants are known to release an extremely high portion of the fixated carbon to the soil, less is known about the composition and role of C-containing compounds in the rhizosphere, in particular those involved in chemical communication...
March 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28333392/the-biosynthesis-of-nitrous-oxide-in-the-green-alga-chlamydomonas-reinhardtii
#2
Maxence Plouviez, David Wheeler, Andy Shilton, Michael A Packer, Patricia A McLenachan, Emanuel Sanz-Luque, Francisco Ocaña-Calahorro, Emilio Fernández, Benoit Guieysse
Over the last decades, several studies have reported emissions of nitrous oxide (N2 O) from microalgae cultures and aquatic ecosystems characterized by a high level of algal activity (e.g. eutrophic lakes). As N2 O is a potent greenhouse gas (GHG) and an ozone depleting pollutant, these findings suggest that large scale microalgae cultivation (and possibly, natural eutrophic ecosystems) could have significant environmental impacts. Using the model unicellular microalga Chlamydomonas reinhardtii, this study was conducted to investigate the molecular basis of microalgal N2 O synthesis...
March 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28332758/microrna-microrna-complementarity-is-important-for-the-regulation-pattern-of-nfya5-by-mir169-under-dehydration-shock-in-arabidopsis
#3
Qingguo Du, Meng Zhao, Wei Gao, Suzhen Sun, Wen-Xue Li
MicroRNAs regulate gene expression at the mRNA and translational levels. Although our previous research showed that expression of miR169 and one of its targets, NFYA5, is down- and up-regulated by drought stress, respectively, the current study shows that expression of both miR169 and NFYA5 are induced by dehydration shock. Unlike overexpression of MIR169a/b, overexpression of MIR169i/l did not decrease NFYA5 transcripts but increased NFYA5 protein levels. NFYA5 protein abundance also increased in mir169a knock-out mutants and 35S::MIR169l mir169a double mutants...
March 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28332757/selective-modes-determine-evolutionary-rates-gene-compactness-and-expression-patterns-in-brassica
#4
Yue Guo, Jing Liu, Jiefu Zhang, Shengyi Liu, Jianchang Du
It has been well documented that most nuclear protein-coding genes in organisms can be classified into two categories, i.e., positively selected genes (PSGs) and negatively selected genes (NSGs). The characteristics and evolutionary fates of different types of genes, however, have been poorly understood. In this study, the rates of nonsynonymous substitution (Ka) and the synonymous substitution (Ks) were investigated by comparing the orthologs between the two sequenced Brassica species, Brassica rapa, and Brassica oleracea, and the evolutionary rates, gene structures, expression patterns, and codon bias were compared between PSGs and NSGs...
March 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28332746/global-analysis-of-canola-genes-targeted-by-short-hypocotyl-under-blue-1-during-endosperm-and-embryo-development
#5
Huanan Zhang, Feng Cheng, Yu-Guo Xiao, Xiao-Jun Kang, Xiaowu Wang, Rui Kuang, Min Ni
Seed development in dicots undergoes an early endosperm proliferation, followed by the growth of embryo to replace the endosperm. Endosperm proliferation in dicots not only provides nutrient supplies for subsequent embryo development but also enforces a space limitation to influence the final seed size. Overexpression of Arabidopsis SHORT HYPOCOTYL UNDER BLUE1::GUS (SHB1:GUS) in canola produced large seeds. We performed global analysis of canola genes that were expressed and influenced by SHB1 during early endosperm proliferation at 8 days after pollination (DAP) and late embryo development at 13 DAP...
March 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28321936/jasmonate-inhibits-cop1-activity-to-suppress-hypocotyl-elongation-and-promote-cotyledon-opening-in-etiolated-arabidopsis-seedlings
#6
Yuyu Zheng, Xuefei Cui, Liang Su, Shuang Fang, Jinfang Chu, Qingqiu Gong, Jianping Yang, Ziqiang Zhu
A germinating seedling undergoes skotomorphogenesis to emerge from the soil and reach for light. During this phase, the cotyledons are closed, and the hypocotyl elongates. Upon exposure to light, the seedling rapidly switches to photomorphogenesis by opening its cotyledons and suppressing hypocotyl elongation. The E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) is critical for maintaining skotomorphogenesis. Here, we report that jasmonate (JA) suppresses hypocotyl elongation and stimulates cotyledon opening in etiolated seedlings, partially phenocopying cop1 mutants in the dark...
March 20, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28321931/disruptions-in-valine-degradation-affect-seed-development-and-germination-in-arabidopsis
#7
Andrew B Gipson, Kyla J Morton, Rachel J Rhee, Szabolcs Simo, Jack A Clayton, Morgan E Perrett, Christiana G Binkley, Erika L Jensen, Dana L Oakes, Matthew F Rouhier, Kerry A Rouhier
We have functionally characterized the role of two putative mitochondrial enzymes in valine degradation using insertional mutants. Prior to this study, the relationship between branched-chain amino acid degradation (named for leucine, valine, and isoleucine) and seed development was limited to leucine catabolism. Using a reverse genetics approach we show that disruptions in the mitochondrial valine degradation pathway affect seed development and germination in Arabidopsis thaliana. A null mutant of 3-hydroxyisobutyryl-CoA hydrolase (CHY4, At4g31810) resulted in an embryo lethal phenotype, while a null mutant of methylmalonate semialdehyde dehydrogenase (MMSD, At2g14170) resulted in seeds with wrinkled coats, decreased storage reserves, elevated valine and leucine, and reduced germination rates...
March 20, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28301688/multiplex-single-cell-quantification-of-rare-rna-transcripts-from-protoplasts-in-a-model-plant-system
#8
Ulhas S Kadam, Burkhard Schulz, Joseph M K Irudayaraj
Here we demonstrate multiplex and simultaneous detection of four different rare RNA species from plant, Arabidopsis thaliana, using surface enhanced Raman spectroscopy and gold nanoprobes at single cell resolution. We show the applicability of nanoparticle-based Raman spectroscopic sensor to study intracellular RNA copies. First, we demonstrate that gold-nanoparticles decorate with Raman probes and carrying specific nucleic acid probe sequences can be uptaken by the protoplasts. We confirm the internalization of gold nanoprobes by TEM, ICP-MS, and fluorescence imaging...
March 16, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28295753/identification-of-stn7-stn8-kinase-targets-reveals-connections-between-electron-transport-metabolism-and-gene-expression
#9
Anna Schönberg, Anja Rödiger, Wiebke Mehwald, Johann Galonska, Gideon Christ, Stefan Helm, Domenika Thieme, Petra Majovsky, Wolfgang Hoehenwarter, Sacha Baginsky
The thylakoid-associated kinases STN7 and STN8 are involved in short- and long-term acclimation of photosynthetic electron transport to changing light conditions. Here we report the identification of STN7/STN8 in vivo targets that connect photosynthetic electron transport with metabolism and gene expression. Comparative phosphoproteomics with the stn7 and stn8 single and double mutants identified two proteases, one RNA-binding protein, a ribosomal protein, the large subunit of rubisco and a ferredoxin-NADP reductase as targets for the thylakoid-associated kinases...
March 14, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28295776/compartmentalisation-of-fefe-hydrogenase-maturation-in-chlamydomonas-reinhardtii
#10
Anne Sawyer, Yu Bai, Yinghua Lu, Anja Hemschemeier, Thomas Happe
Molecular hydrogen (H2 ) can be produced in green microalgae by [FeFe]-hydrogenases as a direct product of photosynthesis. The Chlamydomonas reinhardtii hydrogenase HYDA1 contains a catalytic site comprising a classic [4Fe4S] cluster linked to a unique 2Fe sub-cluster. From in vitro studies it appears that the [4Fe4S] cluster is incorporated first by the housekeeping FeS cluster assembly machinery, followed by the 2Fe sub-cluster, whose biosynthesis requires the specific maturases HYDEF and HYDG. To investigate the maturation process in vivo, we expressed HYDA1 from the C...
March 13, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28295817/plasticity-and-innovation-of-regulatory-mechanisms-underlying-seed-oil-content-mediated-by-duplicated-genes-in-the-palaeopolyploid-soybean
#11
Dajian Zhang, Meixia Zhao, Shuai Li, Lianjun Sun, Weidong Wang, Chunmei Cai, Emily C Dierking, Jianxin Ma
Many plants have undergone whole genome duplication (WGD). However, how regulatory networks underlying a particular trait are reshaped in polyploids has not been experimentally investigated. Here we show that the regulatory pathways modulating seed oil content, which involve WRINKLED1 (WRI1), (LEAFY COTYLEDON1) LEC1, and LEC2 in Arabidopsis, have been modified in the palaeopolyploid soybean. Such modifications include functional reduction of GmWRI1b of the GmWRI1a/GmWRI1b homoeologous pair relevant to WRI1, complementary non-allelic dosage effects of the GmLEC1a/GmLEC1b homoeologous pair relevant to LEC1, pseudogenization of the singleton GmLEC2 relevant to LEC2, and the rise of the LEC2-like function of GmABI3b, contrasting to its homoeolog GmABI3a, which maintains the ABSCISIC ACID INSENSITIVE 3 (ABI3)-like function in modulating seed maturation and dormancy...
March 11, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28276145/ljmot1-a-high-affinity-molybdate-transporter-from-lotus-japonicus-is-essential-for-molybdate-uptake-but-not-for-the-delivery-to-nodules
#12
Guilan Duan, Tsuneo Hakoyama, Takehiro Kamiya, Hiroki Miwa, Fabien Lombardo, Shusei Sato, Satoshi Tabata, Zheng Chen, Toshihiro Watanabe, Takuro Shinano, Toru Fujiwara
Molybdenum (Mo) is an essential nutrient for plants, and is required for nitrogenase activity of legumes. However, the pathways of Mo uptake from soils and then delivery to the nodules have not been characterized in legumes. In this study, we characterized a high-affinity Mo transporter (LjMOT1) from Lotus japonicus. Mo concentrations in an ethyl methanesulfonate-mutagenized line (ljmot1) decreased by 70-95% compared with wild type (WT). By comparing the DNA sequences of four AtMOT1 homologs between mutant and WT lines, one point mutation was found in LjMOT1, which altered Trp(292) to a stop codon; no mutation was found in the other homologous genes...
March 9, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28273406/identification-and-characterization-of-inhibitors-of-udp-glucose-and-udp-sugar-pyrophosphorylases-for-in-vivo-studies
#13
Daniel Decker, Christopher Öberg, Leszek A Kleczkowski
UDP-sugars serve as ultimate precursors in hundreds of glycosylation reactions (e.g. for protein and lipid glycosylation, synthesis of sucrose, cell wall polysaccharides, etc.), underlying an important role of UDP-sugar producing enzymes in cellular metabolism. However, genetic studies on mechanisms of UDP-sugar formation were frequently hampered by reproductive impairment of the resulting mutants, making it difficult to assess an in vivo role of a given enzyme. Here, a chemical library containing 17,500 compounds was separately screened against purified UDP-glucose pyrophosphorylase (UGPase) and UDP-sugar pyrophosphorylase (USPase), both enzymes representing the primary mechanisms of UDP-sugar formation...
March 8, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28273364/a-multidomain-enzyme-with-glycerol-3-phosphate-dehydrogenase-and-phosphatase-activities-is-involved-in-a-chloroplastic-pathway-for-glycerol-synthesis-in-chlamydomonas-reinhardtii
#14
Daniela Morales-Sánchez, Yeongho Kim, Ee Leng Terng, Laura Peterson, Heriberto Cerutti
Understanding the unique features of algal metabolism may be necessary to realize the full potential of algae as feedstock for the production of biofuels and biomaterials. Under nitrogen deprivation, the green alga C. reinhardtii showed substantial triacylglycerol (TAG) accumulation and up-regulation of a gene, GPD2, encoding a multidomain enzyme with a putative phosphoserine phosphatase (PSP) motif fused to glycerol-3-phosphate dehydrogenase (GPD) domains. Canonical GPD enzymes catalyze the synthesis of glycerol-3-phosphate (G3P) by reduction of dihydroxyacetone phosphate (DHAP)...
March 8, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28267253/identification-of-the-phosphorylation-targets-of-symbiotic-receptor-like-kinases-using-a-high-throughput-multiplexed-assay-for-kinase-specificity
#15
Dhileepkumar Jayaraman, Alicia L Richards, Michael S Westphall, Joshua J Coon, Jean-Michel Ané
Detecting the phosphorylation substrates of multiple kinases in a single experiment is a challenge, and new techniques are being developed to overcome this challenge. Here, we utilized a multiplexed assay for kinase specificity (MAKS) to identify the substrates directly and to map the phosphorylation site(s) of plant symbiotic receptor-like kinases. The symbiotic receptor-like kinases Nodulation Receptor-like Kinase (NORK) and Lysin motif domain-containing receptor-like kinase 3 (LYK3) are indispensable for the establishment of root nodule symbiosis...
March 7, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28267232/dcl2-rdr6-dependent-transitive-silencing-of-smxl4-and-smxl5-in-arabidopsis-dcl4-mutants-causes-phloem-transport-defect-and-carbohydrate-over-accumulation
#16
Yu-Yi Wu, Bo-Han Hou, Wen-Chi Lee, Shin-Hua Lu, Chen-Jui Yang, Hervé Vaucheret, Ho-Ming Chen
DICER-LIKE (DCL) enzymes process double-stranded RNA into small RNAs that act as regulators of gene expression. Arabidopsis DCL4 and DCL2 each allow post-transcriptional gene silencing (PTGS) of viruses and transgenes, but primary PTGS-prone DCL4 outcompetes transitive PTGS-prone DCL2 in wild-type plants. This hierarchy likely prevents DCL2 to have detrimental effects on endogenous genes. Indeed, dcl4 mutants exhibit developmental defects and increased sensitivity to genotoxic stress. In this study, the mechanism underlying dcl4 defects was investigated using genetic, biochemical and high-throughput sequencing approaches...
March 7, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28258968/identification-of-a-drimenol-synthase-and-drimenol-oxidase-from-persicaria-hydropiper-involved-in-the-biosynthesis-of-insect-deterrent-drimanes
#17
Maurice Henquet, Neli Prota, Justin J J van der Hooft, Marina Varbanova-Herde, Raymond J M Hulzink, Martin de Vos, Marcel Prins, Michiel T J de Both, Maurice C R Franssen, Harro Bouwmeester, Maarten Jongsma
The sesquiterpenoid polygodial, belonging to the drimane family, has been shown to be an antifeedant for a number of herbivorous insects. It is presumed to be synthesized from farnesyl diphosphate via drimenol, subsequent C-12 hydroxylation, and further oxidations at both C-11 and C-12 to form a dialdehyde. Here, we have identified a drimenol synthase (PhDS) and a cytochrome P450 drimenol oxidase (PhDOX1) from Persicaria hydropiper. Expression of PhDS in yeast and plants resulted in production of drimenol only...
March 4, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28258650/concomitant-loss-of-ndh-complex-related-genes-within-chloroplast-and-nuclear-genomes-in-some-orchids
#18
Choun-Sea Lin, Jeremy J W Chen, Chi-Chou Chiu, Han C W Hsiao, Chen-Jui Yang, Xiao-Hua Jin, James Leebens-Mack, Claude W dePamphilis, Yao-Ting Huang, Ling-Hung Yang, Wan-Jung Chang, Ling Kui, Gane Ka-Shu Wong, Jer-Ming Hu, Wen Wang, Ming-Che Shih
Chloroplast NAD(P)H dehydrogenase-like (NDH) complex consists of ~30 subunits from both the nuclear and chloroplast genomes and is ubiquitous across most land plants. In some orchids, such as Phalaenopsis equestris, Dendrobium officinale and D. catenatum, most of the 11 chloroplast genome encoded ndh genes (cp-ndh) have been lost. Here we investigated whether functional cp-ndh genes have been completely lost in these orchids or whether they have been transferred and retained in the nuclear genomes. Further, we assessed whether both cp-ndh genes and nucleus-encoded NDH-related genes can be lost resulting in the absence of the NDH complex...
March 4, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28257158/dna-methylation-of-retrotransposons-dna-transposons-and-genes-in-sugar-beet-beta-vulgaris-l
#19
Falk Zakrzewski, Martin Schmidt, Mieke Van Lijsebettens, Thomas Schmidt
The methylation of cytosines shapes the epigenetic landscape of plant genomes, coordinates transgenerational epigenetic inheritance, represses activity of transposable elements (TEs), affects gene expression, and, hence, can influence the phenotype. Sugar beet (Beta vulgaris ssp. vulgaris), an important crop that accounts for 30% of the worldwide sugar needs, has a relatively small genome size (758 Mbp) consisting of approximately 485 Mbp repetitive DNA (64%) in particular, satellite DNA, retrotransposons, and DNA transposons...
March 3, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28244250/resolving-fine-grained-dynamics-of-retrotransposons-comparative-analysis-of-inferential-methods-and-genomic-resources
#20
Rimjhim Roy Choudhury, Jean-Marc Neuhaus, Christian Parisod
Transposable elements support genome diversification, but comparison of their proliferation and genomic distribution within and among species is necessary to characterize their role in evolution. Such inferences are challenging because of potential bias with incomplete sampling of repetitive genome regions. Here, using the assembled genome as well as genome skimming datasets in Arabis alpina, we assessed the limits of current approaches inferring the biology of transposable elements. Long terminal repeat-retrotransposons (LTR-RTs) identified in the assembled genome were classified into monophyletic lineages (here called tribes), including families of similar copies in Arabis along with elements from related Brassicaceae...
February 28, 2017: Plant Journal: for Cell and Molecular Biology
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