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Table of Contents

The Plant Cell Online: 26 (12)
Dec 2014

EDITORIAL

  • You have accessRestricted Access
    Plant Physiology and The Plant Cell Go Online Only
    Cathie Martin, Mike Blatt
    Plant Cell Dec 2014, 26 (12) 4561; DOI: https://doi.org/10.1105/tpc.114.133579
  • You have accessRestricted Access
    A Hopefully Not Too Long Goodbye
    Cathie Martin
    Plant Cell Dec 2014, 26 (12) 4562-4563; DOI: https://doi.org/10.1105/tpc.114.135004

IN BRIEF

  • A World Beyond <em>Arabidopsis</em>: Updates on Small RNAs in Plant Development
    You have accessRestricted Access
    A World Beyond Arabidopsis: Updates on Small RNAs in Plant Development
    Nancy R. Hofmann
    Plant Cell Dec 2014, 26 (12) 4564; DOI: https://doi.org/10.1105/tpc.114.134635
  • DNA Methylation in Maize: Toto, I’ve a Feeling We’re Not in <em>Arabidopsis</em> Anymore
    You have accessRestricted Access
    DNA Methylation in Maize: Toto, I’ve a Feeling We’re Not in Arabidopsis Anymore
    Jennifer Mach
    Plant Cell Dec 2014, 26 (12) 4565; DOI: https://doi.org/10.1105/tpc.114.135384
  • Membrane Bound: C2-Domain Abscisic Acid-Related Proteins Help Abscisic Acid Receptors Get Where They Need to Go
    You have accessRestricted Access
    Membrane Bound: C2-Domain Abscisic Acid-Related Proteins Help Abscisic Acid Receptors Get Where They Need to Go
    Jennifer Lockhart
    Plant Cell Dec 2014, 26 (12) 4566; DOI: https://doi.org/10.1105/tpc.114.134411
  • Examining the Molecular Basis of Heterophylly in North American Lake Cress
    You have accessRestricted Access
    Examining the Molecular Basis of Heterophylly in North American Lake Cress
    Kathleen L. Farquharson
    Plant Cell Dec 2014, 26 (12) 4567; DOI: https://doi.org/10.1105/tpc.114.135434

REVIEW

  • Phytochromes: An Atomic Perspective on Photoactivation and Signaling
    You have accessRestricted Access
    Phytochromes: An Atomic Perspective on Photoactivation and Signaling
    E. Sethe Burgie, Richard D. Vierstra
    Plant Cell Dec 2014, 26 (12) 4568-4583; DOI: https://doi.org/10.1105/tpc.114.131623

LARGE-SCALE BIOLOGY ARTICLES

  • An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes
    You have accessRestricted Access
    An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes
    Siwaret Arikit, Rui Xia, Atul Kakrana, Kun Huang, Jixian Zhai, Zhe Yan, Oswaldo Valdés-López, Silvas Prince, Theresa A. Musket, Henry T. Nguyen, Gary Stacey, Blake C. Meyers
    Plant Cell Dec 2014, 26 (12) 4584-4601; DOI: https://doi.org/10.1105/tpc.114.131847

    An extensive analysis of small RNAs in soybean identified many miRNAs and phased, secondary siRNA (phasiRNA) loci; some of these miRNAs were the triggers of the phasiRNA loci.

  • Genetic Perturbation of the Maize Methylome
    You have accessRestricted Access
    Genetic Perturbation of the Maize Methylome
    Qing Li, Steven R. Eichten, Peter J. Hermanson, Virginia M. Zaunbrecher, Jawon Song, Jennifer Wendt, Heidi Rosenbaum, Thelma F. Madzima, Amy E. Sloan, Ji Huang, Daniel L. Burgess, Todd A. Richmond, Karen M. McGinnis, Robert B. Meeley, Olga N. Danilevskaya, Matthew W. Vaughn, Shawn M. Kaeppler, Jeffrey A. Jeddeloh, Nathan M. Springer
    Plant Cell Dec 2014, 26 (12) 4602-4616; DOI: https://doi.org/10.1105/tpc.114.133140

    Genetic analyses of maize genes in DNA methylation pathways reveal differences between maize and Arabidopsis, including evidence that DNA methylation is required for growth and development in maize.

  • Integrated Network Analysis Identifies Fight-Club Nodes as a Class of Hubs Encompassing Key Putative Switch Genes That Induce Major Transcriptome Reprogramming during Grapevine Development
    Open Access
    Integrated Network Analysis Identifies Fight-Club Nodes as a Class of Hubs Encompassing Key Putative Switch Genes That Induce Major Transcriptome Reprogramming during Grapevine Development
    Maria Concetta Palumbo, Sara Zenoni, Marianna Fasoli, Mélanie Massonnet, Lorenzo Farina, Filippo Castiglione, Mario Pezzotti, Paola Paci
    Plant Cell Dec 2014, 26 (12) 4617-4635; DOI: https://doi.org/10.1105/tpc.114.133710

    A small pool of putative switch genes, whose expression is negatively correlated with that of genes outside their community in the network, appear to mark the shift from immature to mature growth.

  • Dissecting the Phenotypic Components of Crop Plant Growth and Drought Responses Based on High-Throughput Image Analysis
    Open Access
    Dissecting the Phenotypic Components of Crop Plant Growth and Drought Responses Based on High-Throughput Image Analysis
    Dijun Chen, Kerstin Neumann, Swetlana Friedel, Benjamin Kilian, Ming Chen, Thomas Altmann, Christian Klukas
    Plant Cell Dec 2014, 26 (12) 4636-4655; DOI: https://doi.org/10.1105/tpc.114.129601

    A framework for high-throughput analysis of phenotypic traits from nondestructive plant imaging is used to dissect phenotypic components of barley growth and crop performance.

  • <em>Arabidopsis</em> Ensemble Reverse-Engineered Gene Regulatory Network Discloses Interconnected Transcription Factors in Oxidative Stress
    You have accessRestricted Access
    Arabidopsis Ensemble Reverse-Engineered Gene Regulatory Network Discloses Interconnected Transcription Factors in Oxidative Stress
    Vanessa Vermeirssen, Inge De Clercq, Thomas Van Parys, Frank Van Breusegem, Yves Van de Peer
    Plant Cell Dec 2014, 26 (12) 4656-4679; DOI: https://doi.org/10.1105/tpc.114.131417

    Applying a combination of algorithms on an Arabidopsis abiotic stress gene expression compendium generated system-wide predictions of transcription regulatory interactions and functional relationships. This joined computational and experimental approach identified a set of transcription factors that highly regulate one another and function in detoxification during oxidative stress.

  • The Root Hair “Infectome” of <em>Medicago truncatula</em> Uncovers Changes in Cell Cycle Genes and Reveals a Requirement for Auxin Signaling in Rhizobial Infection
    Open Access
    The Root Hair “Infectome” of Medicago truncatula Uncovers Changes in Cell Cycle Genes and Reveals a Requirement for Auxin Signaling in Rhizobial Infection
    Andrew Breakspear, Chengwu Liu, Sonali Roy, Nicola Stacey, Christian Rogers, Martin Trick, Giulia Morieri, Kirankumar S. Mysore, Jiangqi Wen, Giles E.D. Oldroyd, J. Allan Downie, Jeremy D. Murray
    Plant Cell Dec 2014, 26 (12) 4680-4701; DOI: https://doi.org/10.1105/tpc.114.133496

    Transcriptome profiling of M. truncatula root hairs during the initial stages of rhizobial infection helps to interpret two decades of research on Medicago and provides a foundation for future studies on host-symbiont interactions in the rhizosphere.

RESEARCH ARTICLES

  • The <em>dicer-like1</em> Homolog <em>fuzzy tassel</em> Is Required for the Regulation of Meristem Determinacy in the Inflorescence and Vegetative Growth in Maize
    Open Access
    The dicer-like1 Homolog fuzzy tassel Is Required for the Regulation of Meristem Determinacy in the Inflorescence and Vegetative Growth in Maize
    Beth E. Thompson, Christine Basham, Reza Hammond, Queying Ding, Atul Kakrana, Tzuu-Fen Lee, Stacey A. Simon, Robert Meeley, Blake C. Meyers, Sarah Hake
    Plant Cell Dec 2014, 26 (12) 4702-4717; DOI: https://doi.org/10.1105/tpc.114.132670

    The maize fuzzy tassel mutant is the first dcl1 mutant reported in a plant other than Arabidopsis and enables functional analysis of specific miRNAs and their targets.

  • Transcriptomic Analyses Indicate That Maize Ligule Development Recapitulates Gene Expression Patterns That Occur during Lateral Organ Initiation
    Open Access
    Transcriptomic Analyses Indicate That Maize Ligule Development Recapitulates Gene Expression Patterns That Occur during Lateral Organ Initiation
    Robyn Johnston, Minghui Wang, Qi Sun, Anne W. Sylvester, Sarah Hake, Michael J. Scanlon
    Plant Cell Dec 2014, 26 (12) 4718-4732; DOI: https://doi.org/10.1105/tpc.114.132688

    Microdissection of maize leaf primordia reveals that genes utilized during initiation of leaves and branches are redeployed at the ligule blade-sheath boundary.

  • Regulation of the KNOX-GA Gene Module Induces Heterophyllic Alteration in North American Lake Cress
    You have accessRestricted Access
    Regulation of the KNOX-GA Gene Module Induces Heterophyllic Alteration in North American Lake Cress
    Hokuto Nakayama, Naomi Nakayama, Sumer Seiki, Mikiko Kojima, Hitoshi Sakakibara, Neelima Sinha, Seisuke Kimura
    Plant Cell Dec 2014, 26 (12) 4733-4748; DOI: https://doi.org/10.1105/tpc.114.130229

    A gene module responsible for morphological diversification of leaf form within a species may have been co-opted during plant evolution to regulate morphological variation among species.

  • Site-Specific <em>N-</em>Glycosylation of the S-Locus Receptor Kinase and Its Role in the Self-Incompatibility Response of the Brassicaceae
    You have accessRestricted Access
    Site-Specific N-Glycosylation of the S-Locus Receptor Kinase and Its Role in the Self-Incompatibility Response of the Brassicaceae
    Masaya Yamamoto, Titima Tantikanjana, Takeshi Nishio, Mikhail E. Nasrallah, June B. Nasrallah
    Plant Cell Dec 2014, 26 (12) 4749-4762; DOI: https://doi.org/10.1105/tpc.114.131987

    N-glycosylation of the S-locus receptor kinase ensures its localization to the stigma epidermal cell membrane, where it interacts with its pollen coat-localized ligand to inhibit self-pollination.

  • Proteasome-Mediated Degradation of FRIGIDA Modulates Flowering Time in <em>Arabidopsis</em> during Vernalization
    You have accessRestricted Access
    Proteasome-Mediated Degradation of FRIGIDA Modulates Flowering Time in Arabidopsis during Vernalization
    Xiangyang Hu, Xiangxiang Kong, Chuntao Wang, Lan Ma, Jinjie Zhao, Jingjing Wei, Xiaoming Zhang, Gary J. Loake, Ticao Zhang, Jinling Huang, Yongping Yang
    Plant Cell Dec 2014, 26 (12) 4763-4781; DOI: https://doi.org/10.1105/tpc.114.132738

    Proteasome-mediated protein homeostasis plays a role in the fine-tuning of plant flowering time in response to cold treatment via a series of genetic and epigenetic modifications.

  • Soybean miR172c Targets the Repressive AP2 Transcription Factor NNC1 to Activate <em>ENOD40</em> Expression and Regulate Nodule Initiation
    You have accessRestricted Access
    Soybean miR172c Targets the Repressive AP2 Transcription Factor NNC1 to Activate ENOD40 Expression and Regulate Nodule Initiation
    Youning Wang, Lixiang Wang, Yanmin Zou, Liang Chen, Zhaoming Cai, Senlei Zhang, Fang Zhao, Yinping Tian, Qiong Jiang, Brett J. Ferguson, Peter M. Gresshoff, Xia Li
    Plant Cell Dec 2014, 26 (12) 4782-4801; DOI: https://doi.org/10.1105/tpc.114.131607

    Induction of miR172c in response to rhizobial inoculation activates ENOD40 expression and nodule formation by repressing an AP2/ERF transcription factor, called NNC1, that acts to inhibit ENOD40 expression.

  • C2-Domain Abscisic Acid-Related Proteins Mediate the Interaction of PYR/PYL/RCAR Abscisic Acid Receptors with the Plasma Membrane and Regulate Abscisic Acid Sensitivity in <em>Arabidopsis</em>
    You have accessRestricted Access
    C2-Domain Abscisic Acid-Related Proteins Mediate the Interaction of PYR/PYL/RCAR Abscisic Acid Receptors with the Plasma Membrane and Regulate Abscisic Acid Sensitivity in Arabidopsis
    Lesia Rodriguez, Miguel Gonzalez-Guzman, Maira Diaz, Americo Rodrigues, Ana C. Izquierdo-Garcia, Marta Peirats-Llobet, Maria A. Fernandez, Regina Antoni, Daniel Fernandez, Jose A. Marquez, Jose M. Mulet, Armando Albert, Pedro L. Rodriguez
    Plant Cell Dec 2014, 26 (12) 4802-4820; DOI: https://doi.org/10.1105/tpc.114.129973

    Subcellular localization of abscisic acid receptors as peripheral proteins in the plasma membrane is mediated in a calcium-dependent manner by C2-domain abscisic acid-related proteins.

  • Cell Differentiation and Development in <em>Arabidopsis</em> Are Associated with Changes in Histone Dynamics at the Single-Cell Level
    Open Access
    Cell Differentiation and Development in Arabidopsis Are Associated with Changes in Histone Dynamics at the Single-Cell Level
    Stefanie Rosa, Vardis Ntoukakis, Nobuko Ohmido, Ali Pendle, Rita Abranches, Peter Shaw
    Plant Cell Dec 2014, 26 (12) 4821-4833; DOI: https://doi.org/10.1105/tpc.114.133793

    Histone mobility is regulated during development in Arabidopsis roots, being higher in the division zone and lower in stem cells and differentiated cells, mainly due to changes in histone acetylation.

  • The <em>Arabidopsis</em> Cellulose Synthase Complex: A Proposed Hexamer of CESA Trimers in an Equimolar Stoichiometry
    You have accessRestricted Access
    The Arabidopsis Cellulose Synthase Complex: A Proposed Hexamer of CESA Trimers in an Equimolar Stoichiometry
    Joseph L. Hill Jr., Mustafa B. Hammudi, Ming Tien
    Plant Cell Dec 2014, 26 (12) 4834-4842; DOI: https://doi.org/10.1105/tpc.114.131193

    The three plant cellulose synthases of secondary cell wall synthesis are present in an equimolar ratio; this 1:1:1 ratio is a key first step in understanding how the unique properties of plant-based celluloses originate and furthers our understanding of the cellulose synthase complex.

  • BEL1-LIKE HOMEODOMAIN6 and KNOTTED ARABIDOPSIS THALIANA7 Interact and Regulate Secondary Cell Wall Formation via Repression of <em>REVOLUTA</em>
    You have accessRestricted Access
    BEL1-LIKE HOMEODOMAIN6 and KNOTTED ARABIDOPSIS THALIANA7 Interact and Regulate Secondary Cell Wall Formation via Repression of REVOLUTA
    Yuanyuan Liu, Shijun You, Mallorie Taylor-Teeples, Wenhua L. Li, Mathias Schuetz, Siobhan M. Brady, Carl J. Douglas
    Plant Cell Dec 2014, 26 (12) 4843-4861; DOI: https://doi.org/10.1105/tpc.114.128322

    A negatively acting regulatory module in secondary cell wall biosynthesis involving three transcription factors helps maintain metabolic homeostasis.

  • A NAP-AAO3 Regulatory Module Promotes Chlorophyll Degradation via ABA Biosynthesis in <em>Arabidopsis</em> Leaves
    Open Access
    A NAP-AAO3 Regulatory Module Promotes Chlorophyll Degradation via ABA Biosynthesis in Arabidopsis Leaves
    Jiading Yang, Eric Worley, Michael Udvardi
    Plant Cell Dec 2014, 26 (12) 4862-4874; DOI: https://doi.org/10.1105/tpc.114.133769

    The Arabidopsis transcription factor NAP promotes chlorophyll degradation by enhancing transcription of the abscisic acid (ABA) biosynthetic gene AAO3, which leads to increased levels of the senescence-promoting hormone ABA.

  • Stress-Induced Chloroplast Degradation in <em>Arabidopsis</em> Is Regulated via a Process Independent of Autophagy and Senescence-Associated Vacuoles
    You have accessRestricted Access
    Stress-Induced Chloroplast Degradation in Arabidopsis Is Regulated via a Process Independent of Autophagy and Senescence-Associated Vacuoles
    Songhu Wang, Eduardo Blumwald
    Plant Cell Dec 2014, 26 (12) 4875-4888; DOI: https://doi.org/10.1105/tpc.114.133116

    A senescence- and stress-induced pathway for the degradation of chloroplast proteins that is independent of autophagy and senescence-associated vacuoles is described.

  • The <em>Arabidopsis thaliana</em> Homolog of the Helicase RTEL1 Plays Multiple Roles in Preserving Genome Stability
    You have accessRestricted Access
    The Arabidopsis thaliana Homolog of the Helicase RTEL1 Plays Multiple Roles in Preserving Genome Stability
    Julia Recker, Alexander Knoll, Holger Puchta
    Plant Cell Dec 2014, 26 (12) 4889-4902; DOI: https://doi.org/10.1105/tpc.114.132472

    A helicase is required to preserve genome stability in plants, which is likely due to its role in destabilizing various types of DNA loop recombination intermediates.

  • Accessible DNA and Relative Depletion of H3K9me2 at Maize Loci Undergoing RNA-Directed DNA Methylation
    Open Access
    Accessible DNA and Relative Depletion of H3K9me2 at Maize Loci Undergoing RNA-Directed DNA Methylation
    Jonathan I. Gent, Thelma F. Madzima, Rechien Bader, Matthew R. Kent, Xiaoyu Zhang, Maike Stam, Karen M. McGinnis, R. Kelly Dawe
    Plant Cell Dec 2014, 26 (12) 4903-4917; DOI: https://doi.org/10.1105/tpc.114.130427

    Only a small fraction of the maize genome undergoes RNA-directed DNA methylation and, for several characteristics, the chromatin in these areas resembles euchromatin more than heterochromatin.

  • RHON1 Mediates a Rho-Like Activity for Transcription Termination in Plastids of <em>Arabidopsis thaliana</em>
    You have accessRestricted Access
    RHON1 Mediates a Rho-Like Activity for Transcription Termination in Plastids of Arabidopsis thaliana
    Wei Chi, Baoye He, Nikolay Manavski, Juan Mao, Daili Ji, Congming Lu, Jean David Rochaix, Jörg Meurer, Lixin Zhang
    Plant Cell Dec 2014, 26 (12) 4918-4932; DOI: https://doi.org/10.1105/tpc.114.132118

    Genetic and biochemical data reveal that the plastid RNA binding protein RHON1 terminates rbcL transcription, using an ATP-driven mechanism similar to that of Rho factor of bacteria.

  • MicroRNA408 Is Critical for the <em>HY5-SPL7</em> Gene Network That Mediates the Coordinated Response to Light and Copper
    You have accessRestricted Access
    MicroRNA408 Is Critical for the HY5-SPL7 Gene Network That Mediates the Coordinated Response to Light and Copper
    Huiyong Zhang, Xin Zhao, Jigang Li, Huaqing Cai, Xing Wang Deng, Lei Li
    Plant Cell Dec 2014, 26 (12) 4933-4953; DOI: https://doi.org/10.1105/tpc.114.127340

    Changing light and copper conditions jointly regulate the expression of a large cohort of genes; the microRNA MIR408 plays a pivotal role in this regulation.

  • <em>Arabidopsis</em> DPB3-1, a DREB2A Interactor, Specifically Enhances Heat Stress-Induced Gene Expression by Forming a Heat Stress-Specific Transcriptional Complex with NF-Y Subunits
    You have accessRestricted Access
    Arabidopsis DPB3-1, a DREB2A Interactor, Specifically Enhances Heat Stress-Induced Gene Expression by Forming a Heat Stress-Specific Transcriptional Complex with NF-Y Subunits
    Hikaru Sato, Junya Mizoi, Hidenori Tanaka, Kyonosin Maruyama, Feng Qin, Yuriko Osakabe, Kyoko Morimoto, Teppei Ohori, Kazuya Kusakabe, Maika Nagata, Kazuo Shinozaki, Kazuko Yamaguchi-Shinozaki
    Plant Cell Dec 2014, 26 (12) 4954-4973; DOI: https://doi.org/10.1105/tpc.114.132928

    The DNA polymerase II subunit B3-1 interacts with DEHYDRATION-RESPONSIVE ELEMENT BINDING PROTEIN2A and NUCLEAR FACTOR Y proteins to activate gene expression during heat stress responses.

  • The <em>Arabidopsis</em> Abiotic Stress-Induced TSPO-Related Protein Reduces Cell-Surface Expression of the Aquaporin PIP2;7 through Protein-Protein Interactions and Autophagic Degradation
    Open Access
    The Arabidopsis Abiotic Stress-Induced TSPO-Related Protein Reduces Cell-Surface Expression of the Aquaporin PIP2;7 through Protein-Protein Interactions and Autophagic Degradation
    Charles Hachez, Vasko Veljanovski, Hagen Reinhardt, Damien Guillaumot, Celine Vanhee, François Chaumont, Henri Batoko
    Plant Cell Dec 2014, 26 (12) 4974-4990; DOI: https://doi.org/10.1105/tpc.114.134080

    Expression of a plasma membrane aquaporin is regulated by an abiotic stress-induced protein via intracellular protein-protein interactions and targeting of the aquaporin for autophagic degradation.

  • Virulence Factors of Geminivirus Interact with MYC2 to Subvert Plant Resistance and Promote Vector Performance
    You have accessRestricted Access
    Virulence Factors of Geminivirus Interact with MYC2 to Subvert Plant Resistance and Promote Vector Performance
    Ran Li, Berhane T. Weldegergis, Jie Li, Choonkyun Jung, Jing Qu, Yanwei Sun, Hongmei Qian, ChuanSia Tee, Joop J.A. van Loon, Marcel Dicke, Nam-Hai Chua, Shu-Sheng Liu, Jian Ye
    Plant Cell Dec 2014, 26 (12) 4991-5008; DOI: https://doi.org/10.1105/tpc.114.133181

    To attract more disease vectors for viral transmission, geminivirus targets the plant transcription factor MYC2 to suppress plant terpene-based resistance against whitefly.

Teaching Tools in Plant Biology

  • Plant Nutrition 2: Macronutrients (N, P, K, S, Mg, and Ca)
    You have accessRestricted Access
    Plant Nutrition 2: Macronutrients (N, P, K, S, Mg, and Ca)
    Plant Cell Dec 2014, 26 (12) tpc.114.tt1214; DOI: https://doi.org/10.1105/tpc.114.tt1214
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The Plant Cell Online: 26 (12)
The Plant Cell
Vol. 26, Issue 12
Dec 2014
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