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Plant Journal: for Cell and Molecular Biology

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https://www.readbyqxmd.com/read/30407670/the-arabidopsis-rrm-domain-protein-edm3-mediates-race-specific-disease-resistance-by-controlling-h3k9me2-dependent-alternative-polyadenylation-of-rpp7-immune-receptor-transcripts
#1
Yan Lai, Alayne Cuzick, Xueqing Maggie Lu, Jianqiang Wang, Neerja Katiyar, Tokuji Tsuchiya, Karine Le Roch, John M McDowell, Eric Holub, Thomas Eulgem
The NLR-receptor RPP7 mediates race-specific immunity in Arabidopsis. Previous screens for enhanced downy mildew (edm) mutants identified the co-chaperone SGT1b (EDM1) and the PHD-finger protein EDM2 as critical regulators of RPP7. Here, we describe a third edm mutant compromised in RPP7 immunity, edm3. EDM3 encodes a nuclear-localized protein featuring an RNA-recognition motif. Like EDM2, EDM3 promotes histone H3 lysine 9 dimethylation (H3K9me2) at RPP7. Global profiling of H3K9me2 showed EDM3 to affect this silencing mark at a large set of loci...
November 8, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30407665/applying-the-latest-advances-in-genomics-and-phenomics-for-trait-discovery-in-polyploid-wheat
#2
Philippa Borrill, Sophie A Harrington, Cristobal Uauy
Improving traits in wheat has historically been challenging due to its large and polyploid genome, limited genetic diversity, and in-field phenotyping constraints. However, within recent years many of these barriers have been lowered. The availability of a chromosome-level assembly of the wheat genome now facilitates a step-change in wheat genetics and provides a common platform for resources including variation data, gene expression data, and genetic markers. The development of sequenced mutant populations and gene-editing techniques now enable the rapid assessment of gene function in wheat directly...
November 8, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30406958/crispr-cas9-mutagenesis-in-volvox-carteri
#3
José A Ortega-Escalante, Robyn Jasper, Stephen M Miller
Volvox carteri and other volvocine green algae comprise an excellent model for investigating developmental complexity and its origins. Here we describe a method for targeted mutagenesis in V. carteri using CRISPR/Cas9 components expressed from transgenes. We used V. carteri nitrate reductase gene (nitA) regulatory sequences to conditionally express Streptococcus pyogenes Cas9, and V. carteri U6 RNA gene regulatory sequences to constitutively express single-guide RNA (sgRNA) transcripts. V. carteri was bombarded with both the Cas9 vector and with one of several sgRNA vectors programmed to target different test genes (glsA, regA, and invA), and transformants were selected for expression of a hygromycin-resistance marker present on the sgRNA vector...
November 8, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30394623/translational-genomics-using-arabidopsis-as-a-model-enables-the-characterization-of-pennycress-genes-through-forward-and-reverse-genetics
#4
Ratan Chopra, Evan B Johnson, Erin Daniels, Michaela McGinn, Kevin M Dorn, Maliheh Esfahanian, Nicole Folstad, Kirk Amundson, Kayla Altendorf, Kevin Betts, Katherine Frels, James A Anderson, Donald L Wyse, John C Sedbrook, M David Marks
Thlaspi arvense (pennycress) has potential to be domesticated into a new oilseed crop. Information from an extensive body of research on the related plant species, Arabidopsis, can be used to greatly speed this process. Genome-scale comparisons in this report documented that pennycress and Arabidopsis share similar gene duplication. This finding led to the hypothesis that it should be possible to isolate Arabidopsis-like mutants in pennycress. This proved to be true as forward genetic screens identified floral and vegetative pennycress mutants that were similar to mutants found in Arabidopsis...
November 5, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30394608/in-vivo-detection-of-protein-cysteine-sulfenylation-in-plastids
#5
Barbara De Smet, Patrick Willems, Alvaro D Fernandez-Fernandez, Saleh Alseekh, Alisdair R Fernie, Joris Messens, Frank Van Breusegem
Protein cysteine thiols are post-translationally modified under oxidative stress conditions. Illuminated chloroplasts are one of the important sources of hydrogen peroxide (H2 O2 ) and are highly sensitive to environmental stimuli, yet a comprehensive view of the oxidation-sensitive chloroplast proteome is still missing. By targeting the sulfenic acid YAP1C-trapping technology to the plastids of light-grown Arabidopsis cells, we identified 132 putatively sulfenylated plastid proteins upon H2 O2 pulse treatment...
November 5, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30394600/the-role-of-a-class-iii-ga-2-oxidase-in-tomato-internode-elongation
#6
Amanda Schrager-Lavelle, Natalie N Gath, Upendra Kumar Devisetty, Esther Carrera, Isabel López-Díaz, Miguel A Blazquez, Julin N Maloof
A network of environmental inputs and internal signaling controls plant growth, development, and organ elongation. In particular, the growth promoting hormone gibberellin (GA) has been shown to play a significant role in organ elongation. Using tomato as a model organism to study elongation presents an opportunity to study the genetic control of internode specific elongation in a eudicot species with sympodial growth habit and substantial internodes that can and do respond to external stimuli. To investigate internode elongation, a mutant with an elongated hypocotyl and internodes but wild-type petioles was identified through a forward genetic screen...
November 5, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30394596/histone-acetyltransferase-gcn5-contributes-to-cell-wall-integrity-and-salt-stress-tolerance-by-altering-expression-of-cellulose-synthesis-genes
#7
Mei Zheng, Xingbei Liu, Jingchen Lin, Xinye Liu, Zhouying Wang, Mingming Xin, Yingyin Yao, Huiru Peng, Dao-Xiu Zhou, Zhongfu Ni, Qixin Sun, Zhaorong Hu
The excess soluble salts in soil are harmful to most plants growth and development. Evidence is emerging that plant cell wall is involved in sensing of and response to salt stress, but the underlying mechanisms are not well understood. We reveal that histone acetyltransferase GENERAL CONTROL NON-REPRESSED PROTEIN 5 (GCN5) is required for cell wall integrity maintenance and salt stress tolerance. GCN5 mRNA levels are increased in response to salt stress. The gcn5 mutants exhibited severe growth inhibition and cell wall integrity defects under salt stress condition...
November 5, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30375060/cis-regulated-alternative-splicing-divergence-and-its-potential-contribution-to-environmental-responses-in-arabidopsis
#8
Xuncheng Wang, Mei Yang, Diqiu Ren, William Terzaghi, Xing Wang Deng, Guangming He
Alternative splicing (AS) plays key roles in plant development and responses to environmental changes. However, the mechanisms underlying AS divergence (differential expression of transcript isoforms resulting from alternative splicing) in plant accessions and its contributions to responses to environmental stimuli remain unclear. In this study, we investigated genome-wide variation of AS in Arabidopsis thaliana accessions Col-0, Bur-0, C24, Kro-0, and Ler-1, as well as their F1 hybrids, and characterized the regulatory mechanisms for AS divergence by RNA sequencing (RNA-seq)...
October 30, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30375057/extensive-allele-level-remodeling-of-histone-methylation-modification-in-reciprocal-f1-hybrids-of-rice-subspecies
#9
Zhenling Lv, Wenjie Zhang, Ying Wu, Shuangzhan Huang, Yunxiao Zhou, Ai Zhang, Xin Deng, Chunming Xu, Zhengyi Xu, Lei Gong, Bao Liu
Epigenetic mechanism plays a major role in heterosis, partly due to remodeling of epigenetic modifications in the F1 hybrids. Based on ChIP-Seq analyses, we show that, at allele level, extensive histone methylation remodeling occurred for a subset of genomic loci in reciprocal F1 hybrids of rice cultivars, Nipponbare and 93-11, representing the two subspecies, japonica and indica, of rice. Globally, the allele modification-altered loci in leaf or root of the reciprocal F1 hybrids involved ca. 12% to > 43% of genomic regions embarked by either of two typical histone methylation markers, H3K4me3 (> 21,000 genomic regions) and H3K27me3 (> 11,000 genomic regions)...
October 30, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30375131/co-expression-analysis-aids-in-the-identification-of-genes-in-the-cuticular-wax-pathway-in-maize
#10
Jun Zheng, Cheng He, Yang Qin, Guifang Lin, Woojun D Park, Minghao Sun, Jian Li, Xiaoduo Lu, Chunyi Zhang, Cheng-Ting Yeh, Chathura J Gunasekara, Erliang Zeng, Hairong Wei, Patrick S Schnable, Guoying Wang, Sanzhen Liu
Epicuticular waxes provide a hydrophobic barrier that protects land plants from environmental stresses. To elucidate the molecular functions of maize glossy mutants that reduce accumulation of epicuticular waxes, eight non-allelic glossy mutants were subjected to transcriptomic comparisons with their respective wild-type siblings. Transcriptomic comparisons identified 2,279 differential expression (DE) genes. Other glossy genes tended to be down-regulated in glossy mutants; in contrast stress-responsive pathways were induced in mutants...
October 29, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30375064/lignin-characterization-of-rice-coniferaldehyde-5-hydroxylase-loss-of-function-mutants-generated-with-the-crispr-cas9-system
#11
Yuri Takeda, Shiro Suzuki, Yuki Tobimatsu, Keishi Osakabe, Yuriko Osakabe, Safendrri Komara Ragamustari, Masahiro Sakamoto, Toshiaki Umezawa
Aromatic composition of lignin is an important trait that greatly affects the usability of lignocellulosic biomass. We previously identified a rice (Oryza sativa) gene encoding coniferaldehyde 5-hydroxylase (OsCAld5H1), which was effective in modulating syringyl (S)/guaiacyl (G) lignin composition ratio in rice, a model grass species. Previously characterized OsCAld5H1-knockdown rice lines, which were produced via an RNA-interference approach, showed augmented G lignin units yet contained considerable amounts of residual S lignin units...
October 29, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30368955/crop-genome-wide-association-study-a-harvest-of-biological-relevance
#12
Hai-Jun Liu, Jianbing Yan
With the advent of rapid genotyping and next-generation sequencing technologies, genome-wide association study (GWAS) has become a routine strategy for decoding genotype-phenotype associations in many species. More than 1000 such studies over the last decade have revealed substantial genotype-phenotype associations in crops and provided unparalleled opportunities to probe functional genomics. Beyond the many "hits" obtained, this review summarizes recent efforts to increase our understanding of the genetic architecture of complex traits by focusing on non-main effects including epistasis, pleiotropy, and phenotypic plasticity...
October 28, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30362633/cold-stress-response-in-arabidopsis-thaliana-is-mediated-by-gnom-arf-gef
#13
Mohammad Arif Ashraf, Abidur Rahman
Endosomal trafficking plays an important role in regulating plant growth and development both at optimal and stressed conditions. Cold stress response in Arabidopsis root is directly linked to inhibition of the endosomal trafficking of auxin efflux carriers. However, the cellular components that link cold stress and the endosomal trafficking remain elusive. By screening available endosomal trafficking mutants against root growth recovery response under cold stress, we identified GNOM, a SEC7 containing ARF-GEF, as a major modulator of cold response...
October 26, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30362619/fluorescence-in-blue-light-flu-is-involved-in-inactivation-and-localization-ofglutamyl-trna-reductase-during-light-exposure
#14
Zhiwei Hou, YanyuYang, Boris Hedtke, Bernhard Grimm
FLUORESCENT IN BLUE LIGHT (FLU) is anegative regulator involved in dark repression of 5-aminolevulinic acid (ALA) synthesis and interacts with glutamyl-tRNA reductase (GluTR), the rate-limiting enzyme of tetrapyrrole biosynthesis. In this study, we investigatedits regulatory function in light-exposed FLU-overexpressing (FLUOE) Arabidopsis lines and under fluctuating light intensities in wild-type (WT) and fluseedlings. FLUOE lines suppress ALA synthesis in the light resulting in reduced chlorophyll content, but more strongly in low and high light than in medium growth light...
October 26, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30351485/target-of-rapamycin-tor-signaling-modulates-starch-accumulation-via-glycogenin-phosphorylation-status-in-the-unicellular-red-alga-cyanidioschyzon-merolae
#15
Imran Pancha, Hiroki Shima, Nahoko Higashitani, Kazuhiko Igarashi, Atsushi Higashitani, Kan Tanaka, Sousuke Imamura
The target of rapamycin (TOR) signaling pathway is involved in starch accumulation in various eukaryotic organisms; however, the molecular mechanism behind this phenomenon in eukaryotes has not been elucidated. We report a regulatory mechanism of starch accumulation by TOR in the unicellular red alga, Cyanidioschyzon merolae. The starch content in C. merolae after TOR-inactivation by rapamycin, a TOR specific inhibitor, was increased by approximately 10-fold in comparison with its drug vehicle, dimethyl sulfoxide...
October 23, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30351458/leaf-stable-carbon-isotope-composition-reflects-transpiration-efficiency-in-zea-mays
#16
Robert J Twohey, Lucas M Roberts, Anthony J Studer
The increasing demand for food production and predicted climate change scenarios highlight the need for improvements in crop sustainability. The efficient use of water will become increasingly important for rainfed agricultural crops even in fertile regions that have historically received ample precipitation. Improvements in water-use efficiency in Zea mays have been limited, and warrants a renewed effort aided by molecular breeding approaches. Progress has been constrained by the difficulty of measuring water-use in a field environment...
October 23, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30350901/photometric-screens-identified-arabidopsis-peroxisome-proteins-that-impact-photosynthesis-under-dynamic-light-conditions
#17
Jiying Li, Stefanie Tietz, Jeffrey A Cruz, Deserah D Strand, Ye Xu, Jin Chen, David M Kramer, Jianping Hu
Plant peroxisomes function collaboratively with other subcellular organelles, such as chloroplasts and mitochondria, in several metabolic processes. To comprehensively investigate the impact of peroxisomal function on photosynthesis, especially under conditions that are more relevant to natural environments, a systematic screen of over 150 Arabidopsis mutants of genes encoding peroxisomal proteins was conducted using the automated Dynamic Environment Phenotype Imager (DEPI). Dynamic and high light conditions triggered significant photosynthetic defects in a subset of the mutants, including those of photorespiration (PR) and other peroxisomal processes, some of which may also be related to PR...
October 23, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30347487/the-assembly-pathway-of-complex-i-in-arabidopsis-thaliana
#18
Joanna Ligas, Emmanuelle Pineau, Ralph Bock, Martijn A Huynen, Etienne H Meyer
All present-day mitochondria originate from a single endosymbiotic event that gave rise to the last eukaryotic common ancestor (LECA) more than a billion years ago. However, to date, many aspects of mitochondrial evolution have remained unresolved. Comparative genomics and proteomics have revealed a complex evolutionary origin of many mitochondrial components. To understand the evolution of the respiratory chain, we have examined both the components and the mechanisms of the assembly pathway of complex I. Complex I represents the first enzyme of the respiratory chain, and complex I deficiencies have dramatic consequences in both animals and plants...
October 22, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30341835/multi-omics-data-driven-investigations-of-metabolic-diversity-of-plant-triterpenoids
#19
Yi Shang, Sanwen Huang
A vast majority of structurally diverse metabolites play essential roles in mediating the interactions between plants and environments, and constitute a valuable resource for industrial applications. Recent breakthroughs in sequencing technology have greatly accelerated metabolic studies of plant natural products, providing opportunities to investigate the molecular basis underlying the diversity of plant specialized metabolites through large-scale analysis. Here, we focus on the biosynthesis of plant triterpenoids, especially the three diversifying reactions (cyclization, oxidation, and glycosylation) that largely contribute to the structural diversity of triterpenoids...
October 19, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30326542/ectopic-expression-of-argos8-reveals-a-role-for-ethylene-in-root-lodging-resistance-in-maize
#20
Jinrui Shi, Bruce J Drummond, Jeffrey E Habben, Norbert Brugiѐre, Ben P Weers, Salim M Hakimi, H Renee Lafitte, Jeffrey R Schussler, Hua Mo, Mary Beatty, Gina Zastrow-Hayes, Dennis O'Neill
Ethylene plays a critical role in many diverse processes in plant development. Recent studies have demonstrated that overexpressing the maize ARGOS8 gene reduces plant response to ethylene by decreasing ethylene signaling, enhancing grain yield in the transgenic maize plants. The objective of this study was to determine the effects of ethylene on the development of nodal roots which are primarily responsible for root lodging resistance in maize. Exogenously applied ACC, the ethylene precursor 1-aminocyclopropane-1-carboxylic acid, was found to promote nodal root emergence...
October 16, 2018: Plant Journal: for Cell and Molecular Biology
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