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Table of Contents

The Plant Cell Online: 24 (7)
Jul 2012

IN BRIEF

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    An Auxin Influx Transporter Regulates Vascular Patterning in Cotyledons
    Kathleen L. Farquharson
    Plant Cell Jul 2012, 24 (7) 2707; DOI: https://doi.org/10.1105/tpc.112.240710
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    A Refined Model of State Transitions in Plant Thylakoid Membranes
    Nancy R. Hofmann
    Plant Cell Jul 2012, 24 (7) 2708; DOI: https://doi.org/10.1105/tpc.112.240711
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    No More Free Lunch: Using RNA Interference in the Host to Reduce Growth of a Parasitic Plant
    Jennifer Mach
    Plant Cell Jul 2012, 24 (7) 2709; DOI: https://doi.org/10.1105/tpc.112.240712

REVIEW

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    Reproductive Isolation during Domestication
    Hannes Dempewolf, Kathryn A. Hodgins, Sonja E. Rummell, Norman C. Ellstrand, Loren H. Rieseberg
    Plant Cell Jul 2012, 24 (7) 2710-2717; DOI: https://doi.org/10.1105/tpc.112.100115

LARGE-SCALE BIOLOGY ARTICLE

  • Open Access
    Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis
    Wenli Zhang, Tao Zhang, Yufeng Wu, Jiming Jiang
    Plant Cell Jul 2012, 24 (7) 2719-2731; DOI: https://doi.org/10.1105/tpc.112.098061

    This article reports high-resolution mapping of the genomic locations that are hypersensitive to DNase I digestion (DH sites) in Arabidopsis thaliana. The DH site data sets in combination with known or putative protein binding motifs and gene expression data sets can be used to reveal protein binding footprints within a specific genomic region.

RESEARCH ARTICLES

  • Open Access
    Pod Corn Is Caused by Rearrangement at the Tunicate1 Locus
    Jong-Jin Han, David Jackson, Robert Martienssen
    Plant Cell Jul 2012, 24 (7) 2733-2744; DOI: https://doi.org/10.1105/tpc.112.100537

    Pod corn (Zea mays), once considered as ancestral to cultivated maize, has a striking phenotype in which each kernel is enclosed with chaff. This phenotype is explained by a chromosomal rearrangement at the Tunicate1 (Tu1) locus that alters the expression pattern of the Tu1 MADS box gene involved in determining floral organ identity.

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    A Genome-Wide Regulatory Framework Identifies Maize Pericarp Color1 Controlled Genes
    Kengo Morohashi, María Isabel Casas, Maria Lorena Falcone Ferreyra, María Katherine Mejía-Guerra, Lucille Pourcel, Alper Yilmaz, Antje Feller, Bruna Carvalho, Julia Emiliani, Eduardo Rodriguez, Silvina Pellegrinet, Michael McMullen, Paula Casati, Erich Grotewold
    Plant Cell Jul 2012, 24 (7) 2745-2764; DOI: https://doi.org/10.1105/tpc.112.098004

    This study combines high-throughput RNA sequencing and chromatin immunoprecipitation and sequencing to examine the effect of Pericarp Color1 (P1) on global gene expression in maize pericarps and silks, finding that, in addition to regulating flavonoid biosynthesis genes, P1 modulates the expression of a much larger gene set involved in primary metabolism and production of other specialized compounds.

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    Cyclic Peptides Arising by Evolutionary Parallelism via Asparaginyl-Endopeptidase–Mediated Biosynthesis
    Joshua S. Mylne, Lai Yue Chan, Aurelie H. Chanson, Norelle L. Daly, Hanno Schaefer, Timothy L. Bailey, Philip Nguyencong, Laura Cascales, David J. Craik
    Plant Cell Jul 2012, 24 (7) 2765-2778; DOI: https://doi.org/10.1105/tpc.112.099085

    To produce highly stable peptides, we show that plant evolution has favored the involvement of a specific protease as well as a similar type of biosynthesis to cut and process peptides to be cyclic from many different precursor proteins. Using Momordica cochinchinensis, we describe the biosynthesis of knotted peptides with cyclic and noncyclic topologies from precursors encoding up to eight peptides.

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    Evidence for a Role of Arabidopsis CDT1 Proteins in Gametophyte Development and Maintenance of Genome Integrity
    Séverine Domenichini, Moussa Benhamed, Geert De Jaeger, Eveline Van De Slijke, Sophie Blanchet, Mickaël Bourge, Lieven De Veylder, Catherine Bergounioux, Cécile Raynaud
    Plant Cell Jul 2012, 24 (7) 2779-2791; DOI: https://doi.org/10.1105/tpc.112.100156

    Loss of function analysis reveals that the replication licensing factors CDT1a and CDT1b act redundantly during gametophyte development. In addition, reduced expression of these genes causes endogenous DNA stress in plants and results in spontaneous mutations, demonstrating that these two proteins are crucial to the maintenance of genome integrity both in vegetative and in reproductive cells.

  • Open Access
    Downregulation of the δ-Subunit Reduces Mitochondrial ATP Synthase Levels, Alters Respiration, and Restricts Growth and Gametophyte Development in Arabidopsis
    Daniela A. Geisler, Carola Päpke, Toshihiro Obata, Adriano Nunes-Nesi, Annemarie Matthes, Kay Schneitz, Eugenia Maximova, Wagner L. Araújo, Alisdair R. Fernie, Staffan Persson
    Plant Cell Jul 2012, 24 (7) 2792-2811; DOI: https://doi.org/10.1105/tpc.112.099424

    The mitochondrial ATP synthase is central to the cell’s energy metabolism. By disturbing the functionality of the ATP synthase, this work identified major short- and long-term changes to metabolite, transcript, and protein levels that led to delayed growth and reduced fertility. It provides new evidence that primary metabolism and gametophyte development seem to be linked by redox and biotic stress signaling.

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    A Light-Regulated Genetic Module Was Recruited to Carpel Development in Arabidopsis following a Structural Change to SPATULA
    Mathieu C. Reymond, Géraldine Brunoud, Aurélie Chauvet, Jaime F. Martínez-Garcia, Marie-Laure Martin-Magniette, Françoise Monéger, Charles P. Scutt
    Plant Cell Jul 2012, 24 (7) 2812-2825; DOI: https://doi.org/10.1105/tpc.112.097915

    This study provides insight into the evolution of flowering plants by demonstrating that a mechanism that modulates carpel margin development in Arabidopsis was recruited from light-regulated processes.

  • Open Access
    The Time Required for Dormancy Release in Arabidopsis Is Determined by DELAY OF GERMINATION1 Protein Levels in Freshly Harvested Seeds
    Kazumi Nakabayashi, Melanie Bartsch, Yong Xiang, Emma Miatton, Silke Pellengahr, Ryoichi Yano, Mitsunori Seo, Wim J.J. Soppe
    Plant Cell Jul 2012, 24 (7) 2826-2838; DOI: https://doi.org/10.1105/tpc.112.100214

    Seed dormancy prevents germination of freshly harvested seeds and is slowly released during seed storage by an unknown mechanism. This work shows that posttranslational modifications of the Arabidopsis thaliana protein DELAY OF GERMINATION1 occurring during seed storage can explain dormancy release.

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    Nuclear Ribosome Biogenesis Mediated by the DIM1A rRNA Dimethylase Is Required for Organized Root Growth and Epidermal Patterning in Arabidopsis
    Yana Wieckowski, John Schiefelbein
    Plant Cell Jul 2012, 24 (7) 2839-2856; DOI: https://doi.org/10.1105/tpc.112.101022

    Analysis of a root epidermal patterning mutant suggests a link between the regulation of translation and cell differentiation. The inability of this mutant to properly methylate its 18S rRNA leads to several developmental defects, including a failure to establish appropriate cell type–specific gene expression programs.

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    Convergent Starvation Signals and Hormone Crosstalk in Regulating Nutrient Mobilization upon Germination in Cereals
    Ya-Fang Hong, Tuan-Hua David Ho, Chin-Feng Wu, Shin-Lon Ho, Rong-Hwei Yeh, Chung-An Lu, Peng-Wen Chen, Lin-Chih Yu, Annlin Chao, Su-May Yu
    Plant Cell Jul 2012, 24 (7) 2857-2873; DOI: https://doi.org/10.1105/tpc.112.097741

    This work shows that not only sugar but also nitrogen and phosphate starvation signals converge with GA signaling to promote the co-nuclear import of MYBS1 and MYBGA and expression of a large set of GA-inducible but functionally distinct hydrolases, transporters, and regulators active in nutrient mobilization required for seedling growth in rice and barley.

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    AUX/LAX Genes Encode a Family of Auxin Influx Transporters That Perform Distinct Functions during Arabidopsis Development
    Benjamin Péret, Kamal Swarup, Alison Ferguson, Malvika Seth, Yaodong Yang, Stijn Dhondt, Nicholas James, Ilda Casimiro, Paula Perry, Adnan Syed, Haibing Yang, Jesica Reemmer, Edward Venison, Caroline Howells, Miguel A. Perez-Amador, Jeonga Yun, Jose Alonso, Gerrit T.S. Beemster, Laurent Laplaze, Angus Murphy, Malcolm J. Bennett, Erik Nielsen, Ranjan Swarup
    Plant Cell Jul 2012, 24 (7) 2874-2885; DOI: https://doi.org/10.1105/tpc.112.097766

    This article describes the role of AUX/LAX auxin influx carriers in plant development, revealing that the auxin influx carrier LAX2 regulates vascular patterning in cotyledons. Although the AUX1/LAX family members share auxin transport characteristics, these transport activities seem to be dependent on their unique cell- or tissue-type expression patterns.

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    The Transcription Factors BEL1 and SPL Are Required for Cytokinin and Auxin Signaling During Ovule Development in Arabidopsis
    Stefano Bencivenga, Sara Simonini, Eva Benková, Lucia Colombo
    Plant Cell Jul 2012, 24 (7) 2886-2897; DOI: https://doi.org/10.1105/tpc.112.100164

    This article examines the role of cytokinin in ovule patterning, finding that cytokinin acts through the auxin efflux facilitator PIN1 and requires the transcription factors BEL1 and SPL/NZZ for proper patterning of the ovule.

  • Open Access
    The Arabidopsis Mediator Subunit MED25 Differentially Regulates Jasmonate and Abscisic Acid Signaling through Interacting with the MYC2 and ABI5 Transcription Factors
    Rong Chen, Hongling Jiang, Lin Li, Qingzhe Zhai, Linlin Qi, Wenkun Zhou, Xiaoqiang Liu, Hongmei Li, Wenguang Zheng, Jiaqiang Sun, Chuanyou Li
    Plant Cell Jul 2012, 24 (7) 2898-2916; DOI: https://doi.org/10.1105/tpc.112.098277

    This work describes that the MED25 subunit of the Arabidopsis thaliana Mediator complex positively regulates JA-mediated gene expression through interacting with the transcription factor MYC2. It also describes that MED25 negatively regulates ABA-mediated gene expression through interacting with the transcription factor ABI5.

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    Arabidopsis JAGGED LATERAL ORGANS Acts with ASYMMETRIC LEAVES2 to Coordinate KNOX and PIN Expression in Shoot and Root Meristems
    Madlen I. Rast, Rüdiger Simon
    Plant Cell Jul 2012, 24 (7) 2917-2933; DOI: https://doi.org/10.1105/tpc.112.099978

    This study analyzes the genetic and protein interactions between the two LOB domain proteins JLO and AS2. Both proteins physically interact with each other but are also able to build homomeric complexes. Genetically, functions were identified that are seemingly common to JLO and AS2 in the regulation of KNOX and PIN expression. JLO depends for some of these functions on AS2.

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    PROTON GRADIENT REGULATION5 Is Essential for Proper Acclimation of Arabidopsis Photosystem I to Naturally and Artificially Fluctuating Light Conditions
    Marjaana Suorsa, Sari Järvi, Michele Grieco, Markus Nurmi, Malgorzata Pietrzykowska, Marjaana Rantala, Saijaliisa Kangasjärvi, Virpi Paakkarinen, Mikko Tikkanen, Stefan Jansson, Eva-Mari Aro
    Plant Cell Jul 2012, 24 (7) 2934-2948; DOI: https://doi.org/10.1105/tpc.112.097162

    This work demonstrates that photosystem I, not photosystem II, is susceptible to photodamage under natural fluctuations in light intensity in Arabidopsis thaliana. PGR5 is an indispensable protein for protection of photosystem I, particularly in young plants. PGR5-mediated protection takes place via regulation of linear electron transfer, rather than via cyclic electron transfer.

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    Arabidopsis Phytochrome A Is Modularly Structured to Integrate the Multiple Features That Are Required for a Highly Sensitized Phytochrome
    Yoshito Oka, Yuya Ono, Gabriela Toledo-Ortiz, Keio Kokaji, Minami Matsui, Nobuyoshi Mochizuki, Akira Nagatani
    Plant Cell Jul 2012, 24 (7) 2949-2962; DOI: https://doi.org/10.1105/tpc.111.094201

    This study analyzes a variety of chimeric phytochromes to identify distinct structural modules within the phytochrome A photoreceptor that confer specific properties.

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    Functional Analyses of the Plant Photosystem I–Light-Harvesting Complex II Supercomplex Reveal That Light-Harvesting Complex II Loosely Bound to Photosystem II Is a Very Efficient Antenna for Photosystem I in State II
    Pierre Galka, Stefano Santabarbara, Thi Thu Huong Khuong, Hervé Degand, Pierre Morsomme, Robert C. Jennings, Egbert J. Boekema, Stefano Caffarri
    Plant Cell Jul 2012, 24 (7) 2963-2978; DOI: https://doi.org/10.1105/tpc.112.100339

    State transitions are a photosynthetic response that allows energy distribution balancing between photosystems. Here, a stable PSI-LHCII supercomplex is purified, and it is demonstrated that LHCIIs loosely bound to PSII in State I are the trimers mainly involved in state transitions. Mobile trimers become strongly bound to PSI in State II, and excitation energy transfer to PSI is fast and efficient.

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    N-Terminal Structure of Maize Ferredoxin:NADP+ Reductase Determines Recruitment into Different Thylakoid Membrane Complexes
    Manuel Twachtmann, Bianca Altmann, Norifumi Muraki, Ingo Voss, Satoshi Okutani, Genji Kurisu, Toshiharu Hase, Guy T. Hanke
    Plant Cell Jul 2012, 24 (7) 2979-2991; DOI: https://doi.org/10.1105/tpc.111.094532

    Maize chloroplasts conducting either cyclic or linear electron flow vary in their ferredoxin:NADP+ reductase (FNR) composition. By comparing FNR crystal structures and introducing modified FNRs back into plants, we show that N-terminal structure determines recruitment to different thylakoid complexes. Furthermore, electron flow is analyzed in plants enriched in FNR at alternative locations.

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    A Flavin Binding Cryptochrome Photoreceptor Responds to Both Blue and Red Light in Chlamydomonas reinhardtii
    Benedikt Beel, Katja Prager, Meike Spexard, Severin Sasso, Daniel Weiss, Nico Müller, Mark Heinnickel, David Dewez, Danielle Ikoma, Arthur R. Grossman, Tilman Kottke, Maria Mittag
    Plant Cell Jul 2012, 24 (7) 2992-3008; DOI: https://doi.org/10.1105/tpc.112.098947

    An animal-like cryptochrome (aCRY) functions as a sensory blue light receptor in the green alga Chlamydomonas; in addition, this flavoprotein unexpectedly acts as a sensory red light receptor. For plant cryptochromes, the dark form is proposed to contain an oxidized flavin, whereas for aCRY, the broad spectral responses point to the neutral radical state in the dark.

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    The CRYPTOCHROME1-Dependent Response to Excess Light Is Mediated through the Transcriptional Activators ZINC FINGER PROTEIN EXPRESSED IN INFLORESCENCE MERISTEM LIKE1 and ZML2 in Arabidopsis
    Jehad Shaikhali, Juan de Dios Barajas-Lopéz, Krisztina Ötvös, Dmitry Kremnev, Ana Sánchez Garcia, Vaibhav Srivastava, Gunnar Wingsle, Laszlo Bako, Åsa Strand
    Plant Cell Jul 2012, 24 (7) 3009-3025; DOI: https://doi.org/10.1105/tpc.112.100099

    This work identifies ZML2 and its homolog ZML1 as key regulators of gene expression in the cry1-dependent response to excess light. ZML1/2 bind to the CryR1 cis-element in vitro and in vivo, and T-DNA insertion lines for ZML2 and ZML1 were sensitive to excess light, demonstrating misregulation of several cry1-dependent genes in response to excess light.

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    Chloroplasts of Arabidopsis Are the Source and a Primary Target of a Plant-Specific Programmed Cell Death Signaling Pathway
    Chanhong Kim, Rasa Meskauskiene, Shengrui Zhang, Keun Pyo Lee, Munusamy Lakshmanan Ashok, Karolina Blajecka, Cornelia Herrfurth, Ivo Feussner, Klaus Apel
    Plant Cell Jul 2012, 24 (7) 3026-3039; DOI: https://doi.org/10.1105/tpc.112.100479

    Under mild light stress, plants enhance the production of singlet oxygen that acts as a signal. Singlet oxygen–mediated signaling forms an integral part of photosynthesis that translates environmental variability affecting photosynthetic electron transport into signals that regulate the readjustment of the plant to environmental changes.

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    Differential Transit Peptide Recognition during Preprotein Binding and Translocation into Flowering Plant Plastids
    Prakitchai Chotewutmontri, L. Evan Reddick, David R. McWilliams, Ian M. Campbell, Barry D. Bruce
    Plant Cell Jul 2012, 24 (7) 3040-3059; DOI: https://doi.org/10.1105/tpc.112.098327

    Despite their identification >30 years ago, the mechanism of how chloroplast transit peptides direct precursor import remains enigmatic. This is more confounding in light of emerging genomic data that indicate ∼20% of plant genomes encode chloroplast-targeted proteins. This article develops a heuristic approach that may provide universal criteria for what makes a functional transit peptide.

  • Open Access
    The Core of Chloroplast Nucleoids Contains Architectural SWIB Domain Proteins
    Joanna Melonek, Andrea Matros, Mirl Trösch, Hans-Peter Mock, Karin Krupinska
    Plant Cell Jul 2012, 24 (7) 3060-3073; DOI: https://doi.org/10.1105/tpc.112.099721

    The transcriptionally active chromosome from spinach chloroplasts was analyzed by two-dimensional gel electrophoresis and mass spectrometry to identify proteins involved in structuring of the nucleoid core. SWI/SNF complex B domain–containing proteins were identified that might be functional equivalents of the bacterial nucleoid-associated proteins involved in shaping of nucleoid architecture.

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    BEX5/RabA1b Regulates trans-Golgi Network-to-Plasma Membrane Protein Trafficking in Arabidopsis
    Elena Feraru, Mugurel I. Feraru, Rin Asaoka, Tomasz Paciorek, Riet De Rycke, Hirokazu Tanaka, Akihiko Nakano, Jiří Friml
    Plant Cell Jul 2012, 24 (7) 3074-3086; DOI: https://doi.org/10.1105/tpc.112.098152

    A fluorescence imaging-based forward genetic screen that detects components of endocytic recycling is used to identify BEX5/RabA1b as a regulator of protein trafficking to the plasma membrane.

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    An Essential Pentatricopeptide Repeat Protein Facilitates 5′ Maturation and Translation Initiation of rps3 mRNA in Maize Mitochondria
    Nikolay Manavski, Virginie Guyon, Jörg Meurer, Udo Wienand, Reinhold Brettschneider
    Plant Cell Jul 2012, 24 (7) 3087-3105; DOI: https://doi.org/10.1105/tpc.112.099051

    This work finds that a maize PPR protein (MPPR6) localized to the mitochondria is directly involved in 5′ maturation and translation initiation of rps3 mRNA. This dual role supports a general principle of action for PPR proteins in RNA processing and translation.

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    Reconstitution of Plant Alkane Biosynthesis in Yeast Demonstrates That Arabidopsis ECERIFERUM1 and ECERIFERUM3 Are Core Components of a Very-Long-Chain Alkane Synthesis Complex
    Amélie Bernard, Frédéric Domergue, Stéphanie Pascal, Reinhard Jetter, Charlotte Renne, Jean-Denis Faure, Richard P. Haslam, Johnathan A. Napier, René Lessire, Jérôme Joubès
    Plant Cell Jul 2012, 24 (7) 3106-3118; DOI: https://doi.org/10.1105/tpc.112.099796

    Very-long-chain alkanes are major components of cuticular waxes, a protective layer covering aerial surfaces of plants. This article shows that the Arabidopsis thaliana CER1 protein interacts with the wax-associated CER3 protein and with the cytochrome b5 isoforms found in the endoplasmic reticulum, and that these proteins constitute the enzymatic complex catalyzing the redox-dependent plant alkane synthesis.

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    Tomato GDSL1 Is Required for Cutin Deposition in the Fruit Cuticle
    Anne-Laure Girard, Fabien Mounet, Martine Lemaire-Chamley, Cédric Gaillard, Khalil Elmorjani, Julien Vivancos, Jean-Luc Runavot, Bernard Quemener, Johann Petit, Véronique Germain, Christophe Rothan, Didier Marion, Bénédicte Bakan
    Plant Cell Jul 2012, 24 (7) 3119-3134; DOI: https://doi.org/10.1105/tpc.112.101055

    This study analyzes the mechanism by which cutin is deposited. GDSL1, which belongs to the GDSL esterase/acylhydrolase family of plant proteins, is found to play a key role in cutin deposition during fruit cuticle development.

  • Open Access
    An Engineered Monolignol 4-O-Methyltransferase Depresses Lignin Biosynthesis and Confers Novel Metabolic Capability in Arabidopsis
    Kewei Zhang, Mohammad-Wadud Bhuiya, Jorge Rencoret Pazo, Yuchen Miao, Hoon Kim, John Ralph, Chang-Jun Liu
    Plant Cell Jul 2012, 24 (7) 3135-3152; DOI: https://doi.org/10.1105/tpc.112.101287

    Monolignol oxidative coupling is the primary process in lignin biosynthesis, which requires free phenol of a monolignol to generate active radicals. A 4-O-methyltransferase was created via protein engineering that masks the 4-hydroxyls of monolignols. Expressing this enzyme in Arabidopsis led to a substantial reduction of lignin content and concomitant production of novel phenolic esters.

  • Open Access
    Interspecific RNA Interference of SHOOT MERISTEMLESS-Like Disrupts Cuscuta pentagona Plant Parasitism
    Amos Alakonya, Ravi Kumar, Daniel Koenig, Seisuke Kimura, Brad Townsley, Steven Runo, Helena M. Garces, Julie Kang, Andrea Yanez, Rakefet David-Schwartz, Jesse Machuka, Neelima Sinha
    Plant Cell Jul 2012, 24 (7) 3153-3166; DOI: https://doi.org/10.1105/tpc.112.099994

    The authors demonstrate that parasite gene-specific silencing signals originating from a transgenic host are transferred into the invading parasite, leading to reduced parasite yield, stature, and infectivity. This article also refreshes the debate on the origin of haustoria as the authors use morphological and molecular evidence to show that haustoria have both stem and root characteristics.

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The Plant Cell Online: 24 (7)
The Plant Cell
Vol. 24, Issue 7
Jul 2012
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