The Plant Journal

Cover image for Vol. 88 Issue 5

December 2016

Volume 88, Issue 5

Pages 703–903

  1. Issue Information

    1. Top of page
    2. Issue Information
    3. FEATURED ARTICLE
    4. ORIGINAL ARTICLES
    5. RESOURCE
    6. TECHNICAL ADVANCE
    1. Table of Contents (page 703)

      Version of Record online: 28 DEC 2016 | DOI: 10.1111/tpj.12990

  2. FEATURED ARTICLE

    1. Top of page
    2. Issue Information
    3. FEATURED ARTICLE
    4. ORIGINAL ARTICLES
    5. RESOURCE
    6. TECHNICAL ADVANCE
    1. Identification and characterization of the missing phosphatase on the riboflavin biosynthesis pathway in Arabidopsis thaliana (pages 705–716)

      Na Sa, Renu Rawat, Chelsea Thornburg, Kevin D. Walker and Sanja Roje

      Version of Record online: 17 SEP 2016 | DOI: 10.1111/tpj.13291

      Significance Statement

      Riboflavin (Vitamin B2) is the precursor FMN and FAD, essential co-factors for a wide range of redox reactions. Surprisingly, the physiologically relevant catalyst that dephosphorylates the intermediate ARPP has not been characterized from any organism. Here we demonstrate that 5-amino-6-ribitylamino-2,4(1H,3H) pyrimidinedione 5′-phosphate phosphatase, a plastid enzyme, carries out this step of the riboflavin biosynthesis pathway in plants.

  3. ORIGINAL ARTICLES

    1. Top of page
    2. Issue Information
    3. FEATURED ARTICLE
    4. ORIGINAL ARTICLES
    5. RESOURCE
    6. TECHNICAL ADVANCE
    1. Early nitrogen-deprivation responses in Arabidopsis roots reveal distinct differences on transcriptome and (phospho-) proteome levels between nitrate and ammonium nutrition (pages 717–734)

      Jochen Menz, Zhi Li, Waltraud X. Schulze and Uwe Ludewig

      Version of Record online: 15 SEP 2016 | DOI: 10.1111/tpj.13272

      Significance Statement

      As sessile organisms, plants have to rapidly adapt towards environmental fluctuations and thus also towards changes in supply with the key nutrient nitrogen. In roots of adult Arabidopsis plants adapted either to nitrate or ammonium as nitrogen-form, we found clear differences in the earliest nitrogen deprivation response on transcriptome and (phospho-)proteome level and identified candidates with a potential role in nitrogen signaling.

    2. Apple (Malus domestica) MdERF2 negatively affects ethylene biosynthesis during fruit ripening by suppressing MdACS1 transcription (pages 735–748)

      Tong Li, Zhongyu Jiang, Lichao Zhang, Dongmei Tan, Yun Wei, Hui Yuan, Tianlai Li and Aide Wang

      Version of Record online: 17 SEP 2016 | DOI: 10.1111/tpj.13289

      Significance Statement

      Fruit ripening in climacteric fruit requires the gaseous phytohormone ethylene. Knowledge of the transcriptional regulation of ethylene biosynthesis is still limited. Here we show that an apple (Malus domestica) ethylene response factor, MdERF2, acts as a negative regulator of ethylene biosynthesis and fruit ripening by suppressing the transcription of MdACS1, which encodes 1-aminocyclopropane-1-carboxylic acid synthase, the rate-limiting enzyme for ethylene biosynthesis.

    3. ABA-dependent inhibition of the ubiquitin proteasome system during germination at high temperature in Arabidopsis (pages 749–761)

      Rex Shun Chiu, Shiyue Pan, Rongmin Zhao and Sonia Gazzarrini

      Version of Record online: 22 SEP 2016 | DOI: 10.1111/tpj.13293

      Significance Statement

      The ubiquitin-proteasome system (UPS) degrades proteins that promote seed dormancy to allow seed germination, but how UPS itself is modulated during the dormancy/germination transition is unclear. Here we show that ABA and high temperature inhibit germination under unfavourable growth conditions by repressing the UPS.

    4. The composition of surface wax on trichomes of Arabidopsis thaliana differs from wax on other epidermal cells (pages 762–774)

      Daniela Hegebarth, Christopher Buschhaus, May Wu, David Bird and Reinhard Jetter

      Version of Record online: 17 SEP 2016 | DOI: 10.1111/tpj.13294

      Significance Statement

      Surface properties of different epidermal cells differ. Cuticular wax analyses distinguish between the compositions of lipid mixtures coating Arabidopsis leaf trichomes and neighbouring pavement cells. Integrating wax compositions of different epidermal cell types with gene expression data shows that trichome cells have an autonomous wax biosynthesis machinery and gene candidates involved in the formation of aliphatic chains longer then C32 were identified.

    5. Integrating metabolomics and transcriptomics data to discover a biocatalyst that can generate the amine precursors for alkamide biosynthesis (pages 775–793)

      Ludmila Rizhsky, Huanan Jin, Michael R. Shepard, Harry W. Scott, Alicen M. Teitgen, M. Ann Perera, Vandana Mhaske, Adarsh Jose, Xiaobin Zheng, Matt Crispin, Eve S. Wurtele, Dallas Jones, Manhoi Hur, Elsa Góngora-Castillo, C. Robin Buell, Robert E. Minto and Basil J. Nikolau

      Version of Record online: 27 SEP 2016 | DOI: 10.1111/tpj.13295

      Significance Statement

      The ethnobotanical history of Echinacea species is due to the ability to synthesize alkamide lipids, which have immune, insecticidal, and plant growth modulating properties. Here we used transcriptomicand metabolomic profiling to identify and characterize a broad-range, branched-chain amino acid (BCAA) decarboxylase in the biosynthetic pathway for alkamides.

    6. Histone acetyltransferase general control non-repressed protein 5 (GCN5) affects the fatty acid composition of Arabidopsis thaliana seeds by acetylating fatty acid desaturase3 (FAD3) (pages 794–808)

      Tianya Wang, Jiewen Xing, Xinye Liu, Zhenshan Liu, Yingyin Yao, Zhaorong Hu, Huiru Peng, Mingming Xin, Dao-Xiu Zhou, Yirong Zhang and Zhongfu Ni

      Version of Record online: 17 SEP 2016 | DOI: 10.1111/tpj.13300

      Significance Statement

      Plant oils represent renewable sources of valuable fatty acids for both chemical and health-related industries. Although fatty acid metabolism has been well characterised, the epigenetic regulation of fatty acid biosynthesis remains elusive. Here we show that histone acetylation of a key fatty acid desaturase affects fatty acid composition in Arabidopsis seeds.

    7. MSL1 is a mechanosensitive ion channel that dissipates mitochondrial membrane potential and maintains redox homeostasis in mitochondria during abiotic stress (pages 809–825)

      Chun Pong Lee, Grigory Maksaev, Gregory S. Jensen, Monika W. Murcha, Margaret E. Wilson, Mark Fricker, Ruediger Hell, Elizabeth S. Haswell, A. Harvey Millar and Lee J. Sweetlove

      Version of Record online: 3 NOV 2016 | DOI: 10.1111/tpj.13301

      Significance Statement

      Controlled uncoupling of mitochondria is important to maintain a redox-balanced respiratory chain and minimise reactive oxygen species production. In this study, we demonstrate that MSL1 is an inner mitochondrial membrane ion channel that can function as a fast-acting release valve for excessive membrane potential thereby preventing oxidative stress in the mitochondrial matrix.

    8. A naturally occurring promoter polymorphism of the Arabidopsis FUM2 gene causes expression variation, and is associated with metabolic and growth traits (pages 826–838)

      David Riewe, Hea-Jung Jeon, Jan Lisec, Marc C. Heuermann, Judith Schmeichel, Monique Seyfarth, Rhonda C. Meyer, Lothar Willmitzer and Thomas Altmann

      Version of Record online: 23 SEP 2016 | DOI: 10.1111/tpj.13303

      Significance Statement

      Arabidopsis thaliana and other Brassicaceae contain an additional cytosolic fumarase (FUM2) that functions in carbon assimilation and nitrogen utilization. Here, we identified a naturally occurring InDel promoter polymorphism in the FUM2 gene (AT5G50950) of the European Arabidopsis population. The Insertion allele reduces FUM2 mRNA, enzyme activity and malate to fumarate conversion in natural, mapping and mutant lines and is accessionwide associated with biomass production. Our findings support FUM2's role in diurnal carbon storage and point to a growth advantage for accessions carrying the Col-0 FUM2 allele.

    9. ERIL1, the plant homologue of ERI-1, is involved in the processing of chloroplastic rRNAs (pages 839–853)

      Glykeria Mermigka, Jutta Maria Helm, Ioannis Vlatakis, Heiko Tobias Schumacher, Evgenia Vamvaka and Kriton Kalantidis

      Version of Record online: 5 OCT 2016 | DOI: 10.1111/tpj.13304

      Significance Statement

      In animals, Enhanced-RNAi1 (ERI1) is an exoribonuclease regulator of RNAi and of rRNA maturation. Here we show that the plant homolog, ERIL-1, is a chloroplast protein and that its misexpression affects chloroplast development, likely due to incorrect processing of chloroplast rRNA precursor molecules. In animals, Enhanced-RNAi1 (ERI1) is an exoribonuclease regulator of RNAi and of rRNA maturation. Here we show that the plant homolog, ERIL-1, is a chloroplast protein and that its misexpression affects chloroplast development, likely due to incorrect processing of chloroplast rRNA precursor molecules.

    10. Dynamic chromatin changes associated with de novo centromere formation in maize euchromatin (pages 854–866)

      Handong Su, Yalin Liu, Yong-Xin Liu, Zhenling Lv, Hongyao Li, Shaojun Xie, Zhi Gao, Junling Pang, Xiu-Jie Wang, Jinsheng Lai, James A. Birchler and Fangpu Han

      Version of Record online: 14 OCT 2016 | DOI: 10.1111/tpj.13305

      Significance Statement

      Centromeres are often embedded in heterochromatin-rich and transcriptionally inert regions. Here we investigated two maize de novo centromeres atypically located in euchromatin. The dynamic changes of DNA methylation patterns indicate that seeding of CENH3, the centromere-specific histone, was affected by intrinsic DNA methylation patterns before neocentromere formation and that CENH3 loading can also shape the DNA methylation patterns after de novo centromere formation.

  4. RESOURCE

    1. Top of page
    2. Issue Information
    3. FEATURED ARTICLE
    4. ORIGINAL ARTICLES
    5. RESOURCE
    6. TECHNICAL ADVANCE
    1. A double-mutant collection targeting MAP kinase related genes in Arabidopsis for studying genetic interactions (pages 867–878)

      Shih-Heng Su and Patrick J. Krysan

      Version of Record online: 18 OCT 2016 | DOI: 10.1111/tpj.13292

      Significance Statement

      Mitogen-activated protein kinase cascades are conserved in all eukaryotes, but because of gene redundancy in Arabidopsis, reverse genetic analyses of single mutants for most genes have not yielded phenotypes. Here we describe a community resource of 275 double mutant lines that can be used for diverse phenotypic screens, to potentially uncover genetic interactions and thus improve understanding of the role of MAP kinase signaling in a range of biological processes.

    2. You have full text access to this OnlineOpen article
      The developmental transcriptome atlas of the biofuel crop Camelina sativa (pages 879–894)

      Sateesh Kagale, John Nixon, Yogendra Khedikar, Asher Pasha, Nicholas J. Provart, Wayne E. Clarke, Venkatesh Bollina, Stephen J. Robinson, Cathy Coutu, Dwayne D. Hegedus, Andrew G. Sharpe and Isobel A. P. Parkin

      Version of Record online: 28 DEC 2016 | DOI: 10.1111/tpj.13302

      Significance Statement

      Developing Camelina sativa as a sustainable bioenergy feedstock will require increased crop productivity and oil composition improvements for industrial applications. Genetic and genomic tools are key to such improvements. Here we present a digital atlas detailing the expression of 88% of the annotated genes during plant development. This transcriptome atlas, in combination with the reference genome sequence, can be leveraged to identify functional associations between genes and to understand the regulatory networks underlying developmental processes.

  5. TECHNICAL ADVANCE

    1. Top of page
    2. Issue Information
    3. FEATURED ARTICLE
    4. ORIGINAL ARTICLES
    5. RESOURCE
    6. TECHNICAL ADVANCE
    1. Using fluorescence lifetime microscopy to study the subcellular localization of anthocyanins (pages 895–903)

      Alexandra Chanoca, Brian Burkel, Nik Kovinich, Erich Grotewold, Kevin W. Eliceiri and Marisa S. Otegui

      Version of Record online: 17 SEP 2016 | DOI: 10.1111/tpj.13297

      Significance Statement

      Plants accumulate thousands of compounds derived from primary and specialized metabolic pathways. Analytical tools have been developed to accurately measure such metabolites in extracts, but it is still a significant challenge to establish their location inside plant cells and to determine how they interact with proteins or with the subcellular environment. Here we use anthocyanins to show that fluorescence lifetime imaging microscopy is a useful tool for understanding anthocyanin trafficking and potentially for estimating vacuolar pH inside intact plant cells. We suggest that this approach can also be applied to other autofluorescent plant metabolites.

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