
Cover image

On the Cover: Reconstructed metabolic network of Arabidopsis (Arabidopsis thaliana) based on AraCyc database version 8.0. Dots (nodes) represent reactions or metabolites, and links (edges) represent the direct association between metabolites and their reactions. Twenty-four currency compound nodes and their edges have been removed. Classified metabolites are color coded by the types of compounds: amino acids (pink), carbohydrates (cyan), cofactors (gray), electron carriers (light purple), fatty acids (peach), plant hormones (red), lipids (green), nucleotides (yellow), and specialized metabolites (blue). For a clearer visual illustration of the metabolic network, we included only the main carbon skeletal compounds of reactions found in pathways from the layout information in AraCyc 8.0. Pajek software was used to visualize the network. Cover image credits: Taehyong Kim and Seung Y. Rhee (Department of Plant Biology, Carnegie Institution for Science, Stanford, CA).
Volume 167, Issue 4, April 2015
ON THE INSIDE
On the Inside
COMMENTARY
Interplay of Reactive Oxygen Species and Nitric Oxide: Nitric Oxide Coordinates Reactive Oxygen Species Homeostasis
BREAKTHROUGH TECHNOLOGIES
Multispectral Phloem-Mobile Probes: Properties and Applications
New fluorescent probes allow the study of phloem transport in Arabidopsis.
Relative Mass Defect Filtering of Mass Spectra: A Path to Discovery of Plant Specialized Metabolites
Metabolite masses measured using LC-MS can be sorted into structural classes using relative mass defect filtering to accelerate the annotation of novel metabolites.
RESEARCH REPORTS
Remodeling of the Infection Chamber before Infection Thread Formation Reveals a Two-Step Mechanism for Rhizobial Entry into the Host Legume Root Hair
Legume root hairs remodel the interface with symbiotic rhizobia prior to initiating the tubular-growing infection thread.
Articles
BIOCHEMISTRY AND METABOLISM
Natural Variation in Monoterpene Synthesis in Kiwifruit: Transcriptional Regulation of Terpene Synthases by NAC and ETHYLENE-INSENSITIVE3-Like Transcription Factors
Fruit monoterpene synthesis in kiwifruit is transcriptionally regulated by transcription factors that activate the terpene synthase promoter.
A Small Phospholipase A2-α from Castor Catalyzes the Removal of Hydroxy Fatty Acids from Phosphatidylcholine in Transgenic Arabidopsis Seeds
A castor phospholipase is involved in editing ricinoleic acid from the membrane lipids in transgenic Arabidopsis seeds.
The Role of the Plant-Specific ALTERED XYLOGLUCAN9 Protein in Arabidopsis Cell Wall Polysaccharide O-Acetylation
The Arabidopsis AXY9 gene encodes a plant-specific component of a cell wall polysaccharide acetylation pathway.
Tricin, a Flavonoid Monomer in Monocot Lignification
Tricin, a flavonoid, is a lignification monomer in grasses where it functions as a nucleation site for lignin polymer formation.
Galactose-Depleted Xyloglucan Is Dysfunctional and Leads to Dwarfism in Arabidopsis
Depleting galactose from the cell wall polysaccharide xyloglucan leads to a disruption of diverse cellular and physiological processes involved in normal plant growth.
Establishment of Monitoring Methods for Autophagy in Rice Reveals Autophagic Recycling of Chloroplasts and Root Plastids during Energy Limitation
Autophagy is responsible for the degradation of leaf chloroplasts and root plastids in rice plants and functions during energy limitation caused by interruption of photosynthesis.
CO2-Responsive CONSTANS, CONSTANS-Like, and Time of Chlorophyll a/b Binding Protein Expression1 Protein Is a Positive Regulator of Starch Synthesis in Vegetative Organs of Rice
Starch contents are highly correlated with the expression levels of a CO2-responsive gene which may regulate coordinated expression of starch synthesis genes.
Proteomic Analysis of Lettuce Seed Germination and Thermoinhibition by Sampling of Individual Seeds at Germination and Removal of Storage Proteins by Polyethylene Glycol Fractionation
Methionine metabolism, ethylene production, and isoprenoid biosynthesis are involved in seed germination and thermoinhibition.
CELL BIOLOGY
A Calcium Sensor-Regulated Protein Kinase, CALCINEURIN B-LIKE PROTEIN-INTERACTING PROTEIN KINASE19, Is Required for Pollen Tube Growth and Polarity
A specific protein kinase plays an important role in pollen tube growth and likely participates in Ca2+ homeostasis through the modulation of Ca2+ influx.
FYVE1 Is Essential for Vacuole Biogenesis and Intracellular Trafficking in Arabidopsis
A phospholipid-binding protein regulates intracellular trafficking and vacuole formation.
Turnip mosaic virus Moves Systemically through Both Phloem and Xylem as Membrane-Associated Complexes
Viral replication complexes are found in phloem sieve elements and in xylem vessels.
ECOPHYSIOLOGY AND SUSTAINABILITY
Does Morphological and Anatomical Plasticity during the Vegetative Stage Make Wheat More Tolerant of Water Deficit Stress Than Rice?
Shoot and root morphology and root anatomical plasticity facilitate effective water uptake and use, making wheat more tolerant of water deficit stress than rice.
Identification of the Primary Lesion of Toxic Aluminum in Plant Roots
The primary mechanism of aluminum toxicity was found to be apoplastic, with aluminum binding to the cell wall inhibiting loosening required for root elongation.
Natural Genetic Variation for Acclimation of Photosynthetic Light Use Efficiency to Growth Irradiance in Arabidopsis
Natural variations in photosynthetic acclimation to different growth irradiances, and to a step-wise increase in growth irradiance, allows genetic analysis of this complex phenomenon.
Phene Synergism between Root Hair Length and Basal Root Growth Angle for Phosphorus Acquisition
Long root hairs and shallow basal roots improve phosphorus uptake in common bean more in combination than in isolation.
Evolution of a Double Amino Acid Substitution in the 5-Enolpyruvylshikimate-3-Phosphate Synthase in Eleusine indica Conferring High-Level Glyphosate Resistance
Naturally evolved double mutants in 5-enolpyruvylshikimate-3-phosphate synthase mimic engineered glyphosate-tolerant 5-enolpyruvylshikimate-3-phosphate synthase in crops and confer high-level glyphosate resistance.
GENES, DEVELOPMENT, AND EVOLUTION
The Phenylpropanoid Pathway Is Controlled at Different Branches by a Set of R2R3-MYB C2 Repressors in Grapevine
A set of transcriptional repressors negatively regulates the expression of genes involved in different branches of the phenylpropanoid pathway.
ALTERED MERISTEM PROGRAM1 Suppresses Ectopic Stem Cell Niche Formation in the Shoot Apical Meristem in a Largely Cytokinin-Independent Manner
Suppression of stem cell niche respecification in the shoot meristem periphery is mediated by a putative carboxypeptidase.
Quantitative Trait Locus Mapping Reveals Regions of the Maize Genome Controlling Root System Architecture
Phenotypic variation of maize root system architecture highlights a genetic trade-off between small compact and large, exploratory root systems.
Lotus japonicus Clathrin Heavy Chain1 Is Associated with Rho-Like GTPase ROP6 and Involved in Nodule Formation
A clathrin heavy chain participates in Nod factor signal transduction and infection thread formation in the leguminous symbiosis with rhizobia.
MEMBRANES, TRANSPORT, AND BIOENERGETICS
Reducing the Genetic Redundancy of Arabidopsis PHOSPHATE TRANSPORTER1 Transporters to Study Phosphate Uptake and Signaling
Disruption of four genes severely reduces the active phosphate transport but does not impact phosphate sensing capacities in Arabidopsis.
A Nucleus-Encoded Chloroplast Protein Regulated by Iron Availability Governs Expression of the Photosystem I Subunit PsaA in Chlamydomonas reinhardtii
A nucleus-encoded chloroplast protein, which controls the stability and translation of the messenger RNA encoding the PsaA subunit of Photosystem I, responds post-transcriptionally to iron availability.
Arabidopsis Type I Proton-Pumping Pyrophosphatase Expresses Strongly in Phloem, Where It Is Required for Pyrophosphate Metabolism and Photosynthate Partitioning
The type I H+-PPase is a key component of the sieve element-companion cell complexes and involved in phloem loading in Arabidopsis.
Photoprotection Conferred by Changes in Photosynthetic Protein Levels and Organization during Dehydration of a Homoiochlorophyllous Resurrection Plant
Protection of a homoiochlorophyllous resurrection plant against oxidative damage during dehydration involves changes in the levels and quaternary organization of photosynthetic proteins.
PHOTOSYSTEM II SUBUNIT R Is Required for Efficient Binding of LIGHT-HARVESTING COMPLEX STRESS-RELATED PROTEIN3 to Photosystem II-Light-Harvesting Supercomplexes in Chlamydomonas reinhardtii
Efficient light to heat dissipation in Chlamydomonas reinhardtii requires binding of a stress-related light-harvesting complex protein to photosystem II and associated light-harvesting complexes II.
WRKY42 Modulates Phosphate Homeostasis through Regulating Phosphate Translocation and Acquisition in Arabidopsis
An Arabidopsis transcription factor modulates phosphate homeostasis by regulating phosphate uptake and translocation.
SIGNALING AND RESPONSE
2-Cysteine Peroxiredoxins and Thylakoid Ascorbate Peroxidase Create a Water-Water Cycle That Is Essential to Protect the Photosynthetic Apparatus under High Light Stress Conditions
2-Cys peroxiredoxins and thylakoid ascorbate peroxidase act together to protect plants against high light damage by creating a water-water cycle and restricting light-induced redox signaling.
S-Nitrosylation Positively Regulates Ascorbate Peroxidase Activity during Plant Stress Responses
Nitric oxide positively regulates a key Arabidopsis peroxidase through S-nitrosylation and enhances resistance to oxidative stresses.
The Greening after Extended Darkness1 Is an N-End Rule Pathway Mutant with High Tolerance to Submergence and Starvation
An E3 ligase PRT6 mutant with constitutive expression of hypoxic genes confers tolerance against submergence via sugar conservation as well as resistance to starvation.
Arabidopsis Glutamate Receptor Homolog3.5 Modulates Cytosolic Ca2+ Level to Counteract Effect of Abscisic Acid in Seed Germination
A Ca2+ signal mediated by a glutamate receptor homolog promotes seed germination, opposing the effect of abscisic acid.
Arabidopsis Glutaredoxin S17 and Its Partner, the Nuclear Factor Y Subunit C11/Negative Cofactor 2α, Contribute to Maintenance of the Shoot Apical Meristem under Long-Day Photoperiod
An unusual multidomain glutaredoxin and its protein partner affect plant development and flowering time in relation to photoperiod in Arabidopsis.
UDP-Glucosyltransferase71C5, a Major Glucosyltransferase, Mediates Abscisic Acid Homeostasis in Arabidopsis
A unique UDP-glucosyltransferase plays an important role in ABA homeostasis by glucosylating ABA to ABA-glucose ester.
Priming of Wheat with the Green Leaf Volatile Z-3-Hexenyl Acetate Enhances Defense against Fusarium graminearum But Boosts Deoxynivalenol Production
A green leaf volatile primes wheat for enhanced defense against the hemibiotrophic fungus F. graminearum by boosting jasmonate-related defenses.
SYSTEMS AND SYNTHETIC BIOLOGY
Patterns of Metabolite Changes Identified from Large-Scale Gene Perturbations in Arabidopsis Using a Genome-Scale Metabolic Network
Global patterns of metabolic responses upon single gene perturbations are specific to gene functions, but they are coordinated with characteristics of the perturbed genes.
Integrated Metabolomics and Transcriptomics Reveal Enhanced Specialized Metabolism in Medicago truncatula Root Border Cells
Medicago truncatula border cells contain elevated levels of specialized metabolites that are important in plant-microbe signaling and defense.
FlowerNet: A Gene Expression Correlation Network for Anther and Pollen Development
A network model of global transcriptional interactions, based on clustering of transcriptionally correlated genes using publicly available floral gene expression data sets, provides a community resource for studies of reproductive gene expression.
Site-Specific Nitrosoproteomic Identification of Endogenously S-Nitrosylated Proteins in Arabidopsis
Proteome-wide identification of S-nitrosylated proteins in Arabidopsis by nitrosoproteomic analysis reveals the involvement of S-nitrosylation in diverse signaling pathways.