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Table of Contents

The Plant Cell Online: 25 (12)
Dec 2013

IN BRIEF

  • Out with the Old: The Fate of Obsolete Peroxisomes
    You have accessRestricted Access
    Out with the Old: The Fate of Obsolete Peroxisomes
    Kathleen L. Farquharson
    Plant Cell Dec 2013, 25 (12) 4769; DOI: https://doi.org/10.1105/tpc.113.251210
  • Embracing Diversity: Uncovering the Mechanism Underlying Interhomologous Recombination Bias during Meiosis
    You have accessRestricted Access
    Embracing Diversity: Uncovering the Mechanism Underlying Interhomologous Recombination Bias during Meiosis
    Jennifer Lockhart
    Plant Cell Dec 2013, 25 (12) 4770; DOI: https://doi.org/10.1105/tpc.113.251211
  • A NAC Transcription Factor for Flooding: <em>SHYG</em> Helps Plants Keep Their Leaves in the Air
    You have accessRestricted Access
    A NAC Transcription Factor for Flooding: SHYG Helps Plants Keep Their Leaves in the Air
    Nancy R. Hofmann
    Plant Cell Dec 2013, 25 (12) 4771; DOI: https://doi.org/10.1105/tpc.113.251212
  • Getting There Faster: Genome-Wide Association Studies Point the Way to Increasing Nutritional Values
    You have accessRestricted Access
    Getting There Faster: Genome-Wide Association Studies Point the Way to Increasing Nutritional Values
    Nancy R. Hofmann
    Plant Cell Dec 2013, 25 (12) 4772; DOI: https://doi.org/10.1105/tpc.113.251213

COMMENTARIES

  • The Plant Science Decadal Vision
    Open Access
    The Plant Science Decadal Vision
    Cathie Martin
    Plant Cell Dec 2013, 25 (12) 4773-4774; DOI: https://doi.org/10.1105/tpc.113.251290
  • The Plant Science Decadal Vision: Response to the Martin Commentary
    Open Access
    The Plant Science Decadal Vision: Response to the Martin Commentary
    David Stern, Sally Mackenzie
    Plant Cell Dec 2013, 25 (12) 4775-4776; DOI: https://doi.org/10.1105/tpc.113.251291

LARGE-SCALE BIOLOGY ARTICLES

  • The High Polyphenol Content of Grapevine Cultivar Tannat Berries Is Conferred Primarily by Genes That Are Not Shared with the Reference Genome
    You have accessRestricted Access
    The High Polyphenol Content of Grapevine Cultivar Tannat Berries Is Conferred Primarily by Genes That Are Not Shared with the Reference Genome
    Cecilia Da Silva, Gianpiero Zamperin, Alberto Ferrarini, Andrea Minio, Alessandra Dal Molin, Luca Venturini, Genny Buson, Paola Tononi, Carla Avanzato, Elisa Zago, Eduardo Boido, Eduardo Dellacassa, Carina Gaggero, Mario Pezzotti, Francisco Carrau, Massimo Delledonne
    Plant Cell Dec 2013, 25 (12) 4777-4788; DOI: https://doi.org/10.1105/tpc.113.118810

    The Tannat grape berry is used to produce high-quality wines with an intense purple color and remarkable antioxidant properties. Through reference-guided assembly of the genome combined with de novo assembly of the transcriptome, we found that the variety-specific genes that might contribute substantially to the unique characteristics of the Tannat berry are not present in the reference genome.

  • Abscisic Acid–Responsive Guard Cell Metabolomes of <em>Arabidopsis</em> Wild-Type and <em>gpa1</em> G-Protein Mutants
    You have accessRestricted Access
    Abscisic Acid–Responsive Guard Cell Metabolomes of Arabidopsis Wild-Type and gpa1 G-Protein Mutants
    Xiaofen Jin, Rui-Sheng Wang, Mengmeng Zhu, Byeong Wook Jeon, Reka Albert, Sixue Chen, Sarah M. Assmann
    Plant Cell Dec 2013, 25 (12) 4789-4811; DOI: https://doi.org/10.1105/tpc.113.119800

    The authors performed metabolomics analysis on a time series of guard cell samples treated with abscisic acid (ABA) to follow the dynamics of 85 metabolites potentially involved in ABA signaling. ABA rapidly altered the profiles of numerous metabolites, including other hormones and calcium-mobilizing agents. ABA responses were greater in the wild type than in a G-protein mutant with ABA-hyposensitive stomata.

  • <em>CAROTENOID CLEAVAGE DIOXYGENASE4</em> Is a Negative Regulator of β-Carotene Content in <em>Arabidopsis</em> Seeds
    You have accessRestricted Access
    CAROTENOID CLEAVAGE DIOXYGENASE4 Is a Negative Regulator of β-Carotene Content in Arabidopsis Seeds
    Sabrina Gonzalez-Jorge, Sun-Hwa Ha, Maria Magallanes-Lundback, Laura Ullrich Gilliland, Ailing Zhou, Alexander E. Lipka, Yen-Nhu Nguyen, Ruthie Angelovici, Haining Lin, Jason Cepela, Holly Little, C. Robin Buell, Michael A. Gore, Dean DellaPenna
    Plant Cell Dec 2013, 25 (12) 4812-4826; DOI: https://doi.org/10.1105/tpc.113.119677

    Analysis of natural variation in Arabidopsis identified CAROTENOID CLEAVAGE DIOXYGENASE4 (CCD4) as a major negative regulator of β-carotene content in seeds and senescing leaves. Given that global vitamin A deficiency is due in part to low β-carotene levels in seeds of major food crops, this study suggests that CCDs may be critical targets for enhancing the provitamin A carotenoid levels of food crops.

  • Genome-Wide Analysis of Branched-Chain Amino Acid Levels in <em>Arabidopsis</em> Seeds
    You have accessRestricted Access
    Genome-Wide Analysis of Branched-Chain Amino Acid Levels in Arabidopsis Seeds
    Ruthie Angelovici, Alexander E. Lipka, Nicholas Deason, Sabrina Gonzalez-Jorge, Haining Lin, Jason Cepela, Robin Buell, Michael A. Gore, Dean DellaPenna
    Plant Cell Dec 2013, 25 (12) 4827-4843; DOI: https://doi.org/10.1105/tpc.113.119370

    Genome-wide association studies of free branched-chain amino acids (BCAAs) in Arabidopsis seeds identified BRANCHED-CHAIN AMINO ACID TRANSFERASE2 (BCAT2), one of seven BCATs encoded in the genome, as an important regulator of BCAA natural variation. The mitochondrial localization of BCAT2 is consistent with a catabolic function and highlights the importance of catabolism in determining seed BCAA levels.

RESEARCH ARTICLES

  • The <em>Trans</em>-Acting Short Interfering RNA3 Pathway and NO APICAL MERISTEM Antagonistically Regulate Leaf Margin Development and Lateral Organ Separation, as Revealed by Analysis of an <em>argonaute7</em>/<em>lobed leaflet1</em> Mutant in <em>Medicago</em> <em>truncatula</em>
    Open Access
    The Trans-Acting Short Interfering RNA3 Pathway and NO APICAL MERISTEM Antagonistically Regulate Leaf Margin Development and Lateral Organ Separation, as Revealed by Analysis of an argonaute7/lobed leaflet1 Mutant in Medicago truncatula
    Chuanen Zhou, Lu Han, Chunxiang Fu, Jiangqi Wen, Xiaofei Cheng, Jin Nakashima, Junying Ma, Yuhong Tang, Yang Tan, Million Tadege, Kirankumar S. Mysore, Guangmin Xia, Zeng-Yu Wang
    Plant Cell Dec 2013, 25 (12) 4845-4862; DOI: https://doi.org/10.1105/tpc.113.117788

    This work shows that a mutation of the ARGONAUTE7 ortholog (LOBED LEAFLET1) in Medicago truncatula causes lobed leaf margins and more widely spaced lateral organs. Characterization of the mutant revealed a balanced developmental mechanism involving several regulators that determine the final shape of leaf margin and the separation of lateral organs.

  • ABA-INSENSITIVE3, ABA-INSENSITIVE5, and DELLAs Interact to Activate the Expression of <em>SOMNUS</em> and Other High-Temperature-Inducible Genes in Imbibed Seeds in <em>Arabidopsis</em>
    You have accessRestricted Access
    ABA-INSENSITIVE3, ABA-INSENSITIVE5, and DELLAs Interact to Activate the Expression of SOMNUS and Other High-Temperature-Inducible Genes in Imbibed Seeds in Arabidopsis
    Soohwan Lim, Jeongmoo Park, Nayoung Lee, Jinkil Jeong, Shigeo Toh, Asuka Watanabe, Junghyun Kim, Hyojin Kang, Dong Hwan Kim, Naoto Kawakami, Giltsu Choi
    Plant Cell Dec 2013, 25 (12) 4863-4878; DOI: https://doi.org/10.1105/tpc.113.118604

    The Arabidopsis aba2, abi3, della pentuple, and som mutant seeds germinate even at high temperature. This work shows that ABI3, ABI5, and DELLA target to the SOM promoter and mediate high-temperature signaling to activate the expression of SOM in imbibed seeds.

  • <em>Arabidopsis</em> ERG28 Tethers the Sterol C4-Demethylation Complex to Prevent Accumulation of a Biosynthetic Intermediate That Interferes with Polar Auxin Transport
    You have accessRestricted Access
    Arabidopsis ERG28 Tethers the Sterol C4-Demethylation Complex to Prevent Accumulation of a Biosynthetic Intermediate That Interferes with Polar Auxin Transport
    Alexis Samba Mialoundama, Nurul Jadid, Julien Brunel, Thomas Di Pascoli, Dimitri Heintz, Mathieu Erhardt, Jérôme Mutterer, Marc Bergdoll, Daniel Ayoub, Alain Van Dorsselaer, Alain Rahier, Paul Nkeng, Philippe Geoffroy, Michel Miesch, Bilal Camara, Florence Bouvier
    Plant Cell Dec 2013, 25 (12) 4879-4893; DOI: https://doi.org/10.1105/tpc.113.115576

    Sterol biosynthetic intermediates (SBIs) derived from the sterol C4-demethylation complex tethered by ERG28 represent signaling molecules in mammals and fungi. In Arabidopsis, loss of ERG28 function leads to the accumulation of the previously undetected SBI, 4-carboxy-4-methyl-24-methylenecycloartanol, which inhibits polar auxin transport. Our work provides a link between sterol metabolism and auxin transport.

  • Phosphatidylinositol 4,5-Bisphosphate Influences PIN Polarization by Controlling Clathrin-Mediated Membrane Trafficking in <em>Arabidopsis</em>
    You have accessRestricted Access
    Phosphatidylinositol 4,5-Bisphosphate Influences PIN Polarization by Controlling Clathrin-Mediated Membrane Trafficking in Arabidopsis
    Till Ischebeck, Stephanie Werner, Praveen Krishnamoorthy, Jennifer Lerche, Mónica Meijón, Irene Stenzel, Christian Löfke, Theresa Wiessner, Yang Ju Im, Imara Y. Perera, Tim Iven, Ivo Feussner, Wolfgang Busch, Wendy F. Boss, Thomas Teichmann, Bettina Hause, Staffan Persson, Ingo Heilmann
    Plant Cell Dec 2013, 25 (12) 4894-4911; DOI: https://doi.org/10.1105/tpc.113.116582

    Plant growth follows positional cues provided by the phytohormone auxin. A key determinant of auxin distribution is the asymmetric plasma membrane localization of PIN-auxin transporters, which involves complex endocytotic cycling. Endocytosis and PIN distribution require the regulatory phospholipid, PtdIns(4,5)P2, which is formed by PI4P 5-kinases that themselves display polarized distribution.

  • CELLULOSE SYNTHASE INTERACTIVE3 Regulates Cellulose Biosynthesis in Both a Microtubule-Dependent and Microtubule-Independent Manner in <em>Arabidopsi</em><em>s</em>
    You have accessRestricted Access
    CELLULOSE SYNTHASE INTERACTIVE3 Regulates Cellulose Biosynthesis in Both a Microtubule-Dependent and Microtubule-Independent Manner in Arabidopsis
    Lei Lei, Shundai Li, Juan Du, Logan Bashline, Ying Gu
    Plant Cell Dec 2013, 25 (12) 4912-4923; DOI: https://doi.org/10.1105/tpc.113.116715

    CELLULOSE SYNTHASE INTERACTIVE3 (CSI3) is an important regulator of cellulose biosynthesis and anisotropic growth. Together with CSI1, CSI3 regulates the rate of cellulose biosynthesis in both a microtubule-dependent and microtubule-independent manner in Arabidopsis.

  • Sufficient Amounts of Functional HOP2/MND1 Complex Promote Interhomolog DNA Repair but Are Dispensable for Intersister DNA Repair during Meiosis in <em>Arabidopsis</em>
    You have accessRestricted Access
    Sufficient Amounts of Functional HOP2/MND1 Complex Promote Interhomolog DNA Repair but Are Dispensable for Intersister DNA Repair during Meiosis in Arabidopsis
    Clemens Uanschou, Arnaud Ronceret, Mona Von Harder, Arnaud De Muyt, Daniel Vezon, Lucie Pereira, Liudmila Chelysheva, Wataru Kobayashi, Hitoshi Kurumizaka, Peter Schlögelhofer, Mathilde Grelon
    Plant Cell Dec 2013, 25 (12) 4924-4940; DOI: https://doi.org/10.1105/tpc.113.118521

    This article elucidates molecular details of meiotic DNA repair by analyzing the interhomolog-promoting factor HOP2. The study found that the recombinase DMC1 requires high levels of HOP2 for repair via the homologous chromosome but only minimal amounts to allow the recombinase RAD51 to perform intersister DNA repair, indicating that DMC1 exerts a negative regulatory effect on RAD51, which is alleviated by HOP2.

  • NAC Transcription Factor SPEEDY HYPONASTIC GROWTH Regulates Flooding-Induced Leaf Movement in <em>Arabidopsis</em>
    You have accessRestricted Access
    NAC Transcription Factor SPEEDY HYPONASTIC GROWTH Regulates Flooding-Induced Leaf Movement in Arabidopsis
    Mamoona Rauf, Muhammad Arif, Joachim Fisahn, Gang-Ping Xue, Salma Balazadeh, Bernd Mueller-Roeber
    Plant Cell Dec 2013, 25 (12) 4941-4955; DOI: https://doi.org/10.1105/tpc.113.117861

    In rosette plants, waterlogging triggers an upward (hyponastic) leaf movement that positions the photosynthetically active organs above the rising water level. This work reports the identification of a transcriptional regulator that affects this response by regulating the expression of its direct target gene, ACO5, encoding ACC oxidase, a key enzyme of ethylene biosynthesis.

  • Autophagy-Related Proteins Are Required for Degradation of Peroxisomes in <em>Arabidopsis</em> Hypocotyls during Seedling Growth
    You have accessRestricted Access
    Autophagy-Related Proteins Are Required for Degradation of Peroxisomes in Arabidopsis Hypocotyls during Seedling Growth
    Jimi Kim, Heeeun Lee, Han Nim Lee, Soon-Hee Kim, Kwang Deok Shin, Taijoon Chung
    Plant Cell Dec 2013, 25 (12) 4956-4966; DOI: https://doi.org/10.1105/tpc.113.117960

    This work reveals a function for autophagy in Arabidopsis hypocotyls after germination. By delivering peroxisomes and other cytoplasmic components to the lytic vacuole for degradation, autophagic machinery may help plant cells clean up old organelles for cell remodeling.

  • Highly Oxidized Peroxisomes Are Selectively Degraded via Autophagy in <em>Arabidopsis</em>
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    Highly Oxidized Peroxisomes Are Selectively Degraded via Autophagy in Arabidopsis
    Michitaro Shibata, Kazusato Oikawa, Kohki Yoshimoto, Maki Kondo, Shoji Mano, Kenji Yamada, Makoto Hayashi, Wataru Sakamoto, Yoshinori Ohsumi, Mikio Nishimura
    Plant Cell Dec 2013, 25 (12) 4967-4983; DOI: https://doi.org/10.1105/tpc.113.116947

    Peroxisomes are organelles that generate reactive oxygen species such as hydrogen peroxide. This study shows that peroxisomes damaged by hydrogen peroxide are degraded via autophagy, suggesting that autophagy plays an important role in quality control of peroxisomes.

  • <em>Arabidopsis</em> Chlorophyll Biosynthesis: An Essential Balance between the Methylerythritol Phosphate and Tetrapyrrole Pathways
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    Arabidopsis Chlorophyll Biosynthesis: An Essential Balance between the Methylerythritol Phosphate and Tetrapyrrole Pathways
    Se Kim, Hagen Schlicke, Kalie Van Ree, Kristine Karvonen, Anant Subramaniam, Andreas Richter, Bernhard Grimm, Janet Braam
    Plant Cell Dec 2013, 25 (12) 4984-4993; DOI: https://doi.org/10.1105/tpc.113.119172

    This work provides evidence into how inhibition of the methylerythritol phosphate pathway causes plant death. Chlorophyll is composed of a chlorin ring, generated by the tetrapyrrole pathway, and an isoprenoid tail, made from the methylerythritol phosphate pathway. The data herein demonstrate that stoichiometric balance between these pathways is essential for viability.

  • <em>Arabidopsis</em> Kelch Repeat F-Box Proteins Regulate Phenylpropanoid Biosynthesis via Controlling the Turnover of Phenylalanine Ammonia-Lyase
    Open Access
    Arabidopsis Kelch Repeat F-Box Proteins Regulate Phenylpropanoid Biosynthesis via Controlling the Turnover of Phenylalanine Ammonia-Lyase
    Xuebin Zhang, Mingyue Gou, Chang-Jun Liu
    Plant Cell Dec 2013, 25 (12) 4994-5010; DOI: https://doi.org/10.1105/tpc.113.119644

    Phenylalanine ammonia-lyase (PAL) catalyzes the first rate-limiting step in the phenylpropanoid pathway. Both in vitro and in vivo biochemical and genetic evidence demonstrated that a group of Kelch repeat F-box proteins physically interact with PAL isozymes, mediating their degradation via the ubiquitination-26S proteasome system, thus affecting phenylpropanoid biosynthesis.

  • <em>Arabidopsis</em> Phosphoglycerate Dehydrogenase1 of the Phosphoserine Pathway Is Essential for Development and Required for Ammonium Assimilation and Tryptophan Biosynthesis
    Open Access
    Arabidopsis Phosphoglycerate Dehydrogenase1 of the Phosphoserine Pathway Is Essential for Development and Required for Ammonium Assimilation and Tryptophan Biosynthesis
    Ruben Maximilian Benstein, Katja Ludewig, Sabine Wulfert, Sebastian Wittek, Tamara Gigolashvili, Henning Frerigmann, Markus Gierth, Ulf-Ingo Flügge, Stephan Krueger
    Plant Cell Dec 2013, 25 (12) 5011-5029; DOI: https://doi.org/10.1105/tpc.113.118992

    Biosynthesis of the amino acid serine occurs mainly via photorespiration in plants. This work shows, however, that locally restricted serine biosynthesis via the alternative phosphoserine pathway is required for proper embryo development and leaf initiation, highlighting the importance of cellular resolution when analyzing metabolic pathways.

  • Phosphatidic Acid Interacts with a MYB Transcription Factor and Regulates Its Nuclear Localization and Function in <em>Arabidopsis</em>
    You have accessRestricted Access
    Phosphatidic Acid Interacts with a MYB Transcription Factor and Regulates Its Nuclear Localization and Function in Arabidopsis
    Hongyan Yao, Geliang Wang, Liang Guo, Xuemin Wang
    Plant Cell Dec 2013, 25 (12) 5030-5042; DOI: https://doi.org/10.1105/tpc.113.120162

    Phosphatidic acid has emerged as a class of cellular mediators involved in various cellular and physiological processes. However, little is known about its mechanism of action. This study shows that phosphatidic acid binds to the MYB transcription factor WER and suggests that the interaction is necessary for the nuclear localization of WER and for WER-mediated regulation of root hair formation.

  • Characterization of <em>Solanum tuberosum</em> Multicystatin and the Significance of Core Domains
    You have accessRestricted Access
    Characterization of Solanum tuberosum Multicystatin and the Significance of Core Domains
    Abigail R. Green, Mark S. Nissen, G.N. Mohan Kumar, N. Richard Knowles, ChulHee Kang
    Plant Cell Dec 2013, 25 (12) 5043-5052; DOI: https://doi.org/10.1105/tpc.113.121004

    This study characterizes the structure and significance of the core of potato multicystatin (PMC), a multidomain cysteine protease inhibitor found in the cortical parenchyma tissue of potato tubers. Papain inhibitory properties of native and recombinant PMC containing core domains are affected by pH. It is likely that pH-mediated regulation imparts unique properties to PMC that modulate proteolysis upon wounding and/or infection via inhibiting cysteine proteases.

  • Calcium/Calmodulin-Dependent Protein Kinase Is Negatively and Positively Regulated by Calcium, Providing a Mechanism for Decoding Calcium Responses during Symbiosis Signaling
    Open Access
    Calcium/Calmodulin-Dependent Protein Kinase Is Negatively and Positively Regulated by Calcium, Providing a Mechanism for Decoding Calcium Responses during Symbiosis Signaling
    J. Benjamin Miller, Amitesh Pratap, Akira Miyahara, Liang Zhou, Stephen Bornemann, Richard J. Morris, Giles E.D. Oldroyd
    Plant Cell Dec 2013, 25 (12) 5053-5066; DOI: https://doi.org/10.1105/tpc.113.116921

    This study dissects the regulation of a calcium/calmodulin-dependent protein kinase (CCaMK) during symbiotic signaling and reveals that CCaMK is both negatively and positively regulated by calcium to create a robust molecular switch that is responsive to calcium concentrations associated with both the basal state and with oscillations.

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The Plant Cell Online: 25 (12)
The Plant Cell
Vol. 25, Issue 12
Dec 2013
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