The Plant Journal

Cover image for Vol. 88 Issue 4

November 2016

Volume 88, Issue 4

Pages 519–702

  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 519)

      Version of Record online: 7 DEC 2016 | DOI: 10.1111/tpj.12989

  2. FEATURED ARTICLE

    1. Top of page
    2. Issue Information
    3. FEATURED ARTICLE
    4. ORIGINAL ARTICLES
    5. RESOURCE
    6. TECHNICAL ADVANCE
    1. You have free access to this content
      AtRAD5A is a DNA translocase harboring a HIRAN domain which confers binding to branched DNA structures and is required for DNA repair in vivo (pages 521–530)

      Daniela Kobbe, Andy Kahles, Maria Walter, Tobias Klemm, Anja Mannuss, Alexander Knoll, Manfred Focke and Holger Puchta

      Version of Record online: 17 SEP 2016 | DOI: 10.1111/tpj.13283

      Significance Statement

      DNA lesions such as crosslinks represent obstacles for the replication machinery, but DNA damage tolerance (DDT) pathways allow lesion bypass without requiring direct lesion repair. Here we assessed the so far unknown properties of the HIRAN domain variant of RAD5A of Arabidopsis thaliana, demonstrating DNA structure-specific binding and properties consistent with a function in DNA damage tolerance.

  3. ORIGINAL ARTICLES

    1. Top of page
    2. Issue Information
    3. FEATURED ARTICLE
    4. ORIGINAL ARTICLES
    5. RESOURCE
    6. TECHNICAL ADVANCE
    1. Cell cycle-regulated PLEIADE/AtMAP65-3 links membrane and microtubule dynamics during plant cytokinesis (pages 531–541)

      Alexander Steiner, Katarzyna Rybak, Melina Altmann, Heather E. McFarlane, Susan Klaeger, Ngoc Nguyen, Eva Facher, Alexander Ivakov, Gerhard Wanner, Bernhard Kuster, Staffan Persson, Pascal Braun, Marie-Theres Hauser and Farhah F. Assaad

      Version of Record online: 5 OCT 2016 | DOI: 10.1111/tpj.13275

      Significance Statement

      Cytokinesis requires extensive coordination between cell cycle cues, membrane trafficking and microtubule dynamics. Here we document physical and genetic interactions between membrane (Transport Protein Particle II, TRAPPII tethering complex) and microtubule (microtubule-associated proteins of the PLEIADE/AtMAP65 family) components of cytokinesis and use our results to outline a conceptual framework for their coordination during plant cytokinesis.

    2. Retrograde signalling caused by heritable mitochondrial dysfunction is partially mediated by ANAC017 and improves plant performance (pages 542–558)

      Olivier Van Aken, Ethan Ford, Ryan Lister, Shaobai Huang and A.Harvey Millar

      Version of Record online: 17 OCT 2016 | DOI: 10.1111/tpj.13276

      Significance Statement

      Mitochondria communicate information on their functional status to the nucleus via retrograde signalling, but it was unclear if retrograde signalling in response to constitutive mitochondrial biogenesis defects is mediated by the same pathways as those triggered during acute mitochondrial dysfunction. Here we show that the transcription factor ANAC017 plays a key role in both biogenic and operational mitochondrial retrograde signalling, improving plant growth and productivity.

    3. The importance of SERINE DECARBOXYLASE1 (SDC1) and ethanolamine biosynthesis during embryogenesis of Arabidopsis thaliana (pages 559–569)

      Ian Sofian Yunus, Yu-chi Liu and Yuki Nakamura

      Version of Record online: 17 OCT 2016 | DOI: 10.1111/tpj.13278

      Significance Statement

      Here we show that ethanolamineis essential forembryo development beyond the heart stage in Arabidopsis thaliana.

    4. Antagonistic control of flowering time by functionally specialized poly(A) polymerases in Arabidopsis thaliana (pages 570–583)

      Hjördis Czesnick and Michael Lenhard

      Version of Record online: 16 SEP 2016 | DOI: 10.1111/tpj.13280

      Significance Statement

      The length of the poly(A) tail affects mRNA stability, nuclear export and translation efficiency. Arabidopsis has three isoforms of nuclear poly(A) polymerase (PAPS): PAPS1 plays a major role in organ growth and plant defence. Here we show that PAPS2 and PAPS4 redundantly promote flowering and act antagonistically to PAPS1, which delays flowering. We suggest that modulating the activity of these isoforms fine-tunes the transition to flowering.

    5. Functional conservation and divergence of GmCHLI genes in polyploid soybean (pages 584–596)

      Qing Li, Chao Fang, Zongbiao Duan, Yucheng Liu, Hao Qin, Jixiang Zhang, Peng Sun, Wenbin Li, Guodong Wang and Zhixi Tian

      Version of Record online: 17 SEP 2016 | DOI: 10.1111/tpj.13282

      Significance Statement

      Clarifying how duplicated genes diverge after polyploidy is important for understanding trait determination. Here we show that mutation in either GmCHLI1 or GmCHLI2, encoding the I subunit of magnesium (Mg)-chelatase, results in a chlorophyll-deficient phenotype, because of the formation of hetero-oligomers in polyploidy.

    6. Early changes of gene activity in developing seedlings of Arabidopsis hybrids relative to parents may contribute to hybrid vigour (pages 597–607)

      Anyu Zhu, Ian K. Greaves, Pei-Chuan Liu, Limin Wu, Elizabeth S. Dennis and W. James Peacock

      Version of Record online: 17 SEP 2016 | DOI: 10.1111/tpj.13285

      Significance Statement

      Heterosis, or hybrid vigour, has been extensively exploited to improve crop yield, but the molecular mechanism underlying it is not fully understood. Here we show that thousands of genes, including photosynthesis-related genes, are activated or repressed earlier in hybrids at young seedling stages than in their parents. We suggest that these earlier changes in gene expression could be essential for heterosis.

    7. Ectopic expression of NnPER1, a Nelumbo nucifera 1-cysteine peroxiredoxin antioxidant, enhances seed longevity and stress tolerance in Arabidopsis (pages 608–619)

      Hu-hui Chen, Pu Chu, Yu-liang Zhou, Yu Ding, Yin Li, Jun Liu, Li-wen Jiang and Shang-zhi Huang

      Version of Record online: 17 SEP 2016 | DOI: 10.1111/tpj.13286

      Significance Statement

      Seed longevity is an important trait for crops and is known to be impaired by reactive oxygen species (ROS) during seed desiccation, storage and germination. Here we show that seed-specific NnPER1 (a 1-cysteine peroxiredoxin from sacred lotus) inhibits DNA lesion and lipid peroxidation by detoxifying ROS and thus enhances seed longevity and seed tolerance to abiotic stress.

    8. CRR1 encoding callose synthase functions in ovary expansion by affecting vascular cell patterning in rice (pages 620–632)

      Longzhen Song, Ruci Wang, Li Zhang, Yueming Wang and Shanguo Yao

      Version of Record online: 17 SEP 2016 | DOI: 10.1111/tpj.13287

      Significance Statement

      Elucidating the mechanisms underlying ovary expansion could be beneficial for improving grain yield and quality. Here we characterize a mutant in a callose synthase, and show that callose synthase is important for initial ovary expansion in rice, possibly by affecting the plasmodesmata-mediated permeability of cell fate determinants required for vascular cell differentiation.

    9. Comparative proteomics of cucurbit phloem indicates both unique and shared sets of proteins (pages 633–647)

      Rosa M. Lopez-Cobollo, Ioannis Filippis, Mark H. Bennett and Colin G.N. Turnbull

      Version of Record online: 17 SEP 2016 | DOI: 10.1111/tpj.13288

      Significance Statement

      Cucurbits are phloem model plants partly because sap exudate is easy to collect, but they unusually possess both fascicular phloem (FP) within vascular bundles and additional extrafascicular phloem (EFP), leading to hot debates on the origins of the exudate and uncertainty about the underlying differences between these two systems. Here, comparison of the two proteomes reveals little overlap, suggesting not only spatial separation but functional divergence.

  4. RESOURCE

    1. Top of page
    2. Issue Information
    3. FEATURED ARTICLE
    4. ORIGINAL ARTICLES
    5. RESOURCE
    6. TECHNICAL ADVANCE
    1. Inter-varietal structural variation in grapevine genomes (pages 648–661)

      Maria Francesca Cardone, Pietro D'Addabbo, Can Alkan, Carlo Bergamini, Claudia Rita Catacchio, Fabio Anaclerio, Giorgia Chiatante, Annamaria Marra, Giuliana Giannuzzi, Rocco Perniola, Mario Ventura and Donato Antonacci

      Version of Record online: 16 SEP 2016 | DOI: 10.1111/tpj.13274

      Significance Statement

      Grapes are important for both fruit and wine production. To help identify genomic variations underlying phenotypic differences, we present an inter-varietal atlas of structural variations and single nucleotide variants. Using comparative analyses, we correlated such genomic variations to agronomically relevant phenotypes.

    2. Dynamics of biomass partitioning, stem gene expression, cell wall biosynthesis, and sucrose accumulation during development of Sorghum bicolor (pages 662–680)

      Brian McKinley, William Rooney, Curtis Wilkerson and John Mullet

      Version of Record online: 16 SEP 2016 | DOI: 10.1111/tpj.13269

      Significance Statement

      Energy sorghum is a drought-resilient C4 grass crop, whose large stems, comprised of lignocellulose and sugars, can be converted to biofuels. Optimizing stem composition is a central focus for improving biomass conversion efficiency, but our knowledge of the molecular basis of stem biogenesis, of the partitioning between structural and non-structural carbohydrates, and of the genes involved in cell wall biosynthesis is incomplete. Here we identified and characterized the expression and regulatory dynamics of >200 genes involved in sorghum stem cell wall biology and sugar accumulation. This resource will be useful for engineering sorghum stems to improve conversion to biofuels and bioproducts.

  5. TECHNICAL ADVANCE

    1. Top of page
    2. Issue Information
    3. FEATURED ARTICLE
    4. ORIGINAL ARTICLES
    5. RESOURCE
    6. TECHNICAL ADVANCE
    1. Molecular characterization and targeted quantitative profiling of the sphingolipidome in rice (pages 681–693)

      Toshiki Ishikawa, Yukihiro Ito and Maki Kawai-Yamada

      Version of Record online: 16 SEP 2016 | DOI: 10.1111/tpj.13281

      Significance Statement

      Sphingolipids play vital roles in plants, but the biological implications of their structural diversity remains to be addressed. Here we detail methodological advances for characterizing complex sphingolipid species quantitatively, and demonstrate its utility for profiling tissue-specific sphingolipids and for metabolic fingerprinting of sphingolipid-associated mutants.

    2. Sensitive whole mount in situ localization of small RNAs in plants (pages 694–702)

      Mouli Ghosh Dastidar, Magdalena Mosiolek, Andrea Bleckmann, Thomas Dresselhaus, Michael D. Nodine and Alexis Maizel

      Version of Record online: 15 SEP 2016 | DOI: 10.1111/tpj.13270

      Significance Statement

      Small RNAs regulate gene expression. Although their biogenesis and mode of action are largely understood, we know less about their biological functions. In particular, determining their spatiotemporal expression patterns thus far has relied on indirect detection via reporter constructs or labor-intensive in situ hybridization on sectioned material. Here, we present a quick in situ hybridization protocol for non-sectioned plant tissues, allowing semi-quantitative detection of small RNAs.

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