Volume 152, Issue 2
February 2010
Cover image
Cover image
On the Cover: The cover shows a jigsaw puzzle of Vincent van Gogh's Irises, recognizable but incomplete. This image is meant as an analogy of plant systems biology. To see the big picture, we must understand how all the component parts (gene regulation, proteins, metabolites, ions, changing environmental conditions, etc.) fit together. Updates and research articles in this issue describe progress in applying systems biology approaches to diverse topics of plant biology. Cover photo is by Paul Herzmark and Sheila McCormick (University of California, Berkeley).
ISSN 0032-0889
EISSN 1532-2548
Issue navigation
Volume 152, Issue 2, February 2010
EDITORIALS - FOCUS ISSUE
Plant Systems Biology
Plant Physiology, Volume 152, Issue 2, February 2010, Page 401, https://doi.org/10.1104/pp.110.900314
UPDATES - FOCUS ISSUE
Gene Expression Analysis, Proteomics, and Network Discovery
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 402–410, https://doi.org/10.1104/pp.109.150433
Systems Biology Update: Cell Type-Specific Transcriptional Regulatory Networks
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 411–419, https://doi.org/10.1104/pp.109.148668
Systems Biology of Organ Initiation at the Shoot Apex
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 420–427, https://doi.org/10.1104/pp.109.150409
Metabolic Networks: How to Identify Key Components in the Regulation of Metabolism and Growth
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 428–444, https://doi.org/10.1104/pp.109.150821
A Systems View of Responses to Nutritional Cues in Arabidopsis: Toward a Paradigm Shift for Predictive Network Modeling
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 445–452, https://doi.org/10.1104/pp.109.148502
Signaling between Chloroplasts and the Nucleus: Can a Systems Biology Approach Bring Clarity to a Complex and Highly Regulated Pathway?
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 453–459, https://doi.org/10.1104/pp.109.149070
Bioinformatic and Systems Biology Tools to Generate Testable Models of Signaling Pathways and Their Targets
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 460–469, https://doi.org/10.1104/pp.109.149583
Hope for Humpty Dumpty: Systems Biology of Cellular Signaling
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 470–479, https://doi.org/10.1104/pp.109.151266
Systems Biology Uncovers the Foundation of Natural Genetic Diversity
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 480–486, https://doi.org/10.1104/pp.109.149328
BREAKTHROUGH TECHNOLOGIES - FOCUS ISSUE
AGRONOMICS1: A New Resource for Arabidopsis Transcriptome Profiling
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 487–499, https://doi.org/10.1104/pp.109.150185
BIOINFORMATICS - FOCUS ISSUE
VirtualPlant: A Software Platform to Support Systems Biology Research
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 500–515, https://doi.org/10.1104/pp.109.147025
Research Articles
Epigenetic Regulation of Gene Programs by EMF1 and EMF2 in Arabidopsis
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 516–528, https://doi.org/10.1104/pp.109.143495
Large-Scale Reverse Genetics in Arabidopsis: Case Studies from the Chloroplast 2010 Project
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 529–540, https://doi.org/10.1104/pp.109.148494
Complete Transcriptome of the Soybean Root Hair Cell, a Single-Cell Model, and Its Alteration in Response to Bradyrhizobium japonicum Infection
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 541–552, https://doi.org/10.1104/pp.109.148379
Systematic Localization of the Arabidopsis Core Cell Cycle Proteins Reveals Novel Cell Division Complexes
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 553–565, https://doi.org/10.1104/pp.109.148643
AtMetExpress Development: A Phytochemical Atlas of Arabidopsis Development
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 566–578, https://doi.org/10.1104/pp.109.148031
AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 579–589, https://doi.org/10.1104/pp.109.148817
A Systems Model of Vesicle Trafficking in Arabidopsis Pollen Tubes
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 590–601, https://doi.org/10.1104/pp.109.148700
Subcellular Flux Analysis of Central Metabolism in a Heterotrophic Arabidopsis Cell Suspension Using Steady-State Stable Isotope Labeling
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 602–619, https://doi.org/10.1104/pp.109.151316
ON THE INSIDE
On the Inside
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 620–621, https://doi.org/10.1104/pp.110.900315
BREAKTHROUGH TECHNOLOGIES
Hydrophobin Fusions for High-Level Transient Protein Expression and Purification in Nicotiana benthamiana
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 622–633, https://doi.org/10.1104/pp.109.149021
SCIENTIFIC CORRESPONDENCE
Phosphoenolpyruvate Carboxylase from C4 Leaves Is Selectively Targeted for Inhibition by Anionic Phospholipids
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 634–638, https://doi.org/10.1104/pp.109.150326
BIOCHEMICAL PROCESSES AND MACROMOLECULAR STRUCTURES
A Bifunctional Geranyl and Geranylgeranyl Diphosphate Synthase Is Involved in Terpene Oleoresin Formation in Picea abies
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 639–655, https://doi.org/10.1104/pp.109.144691
An O-Acetylserine(thiol)lyase Homolog with l-Cysteine Desulfhydrase Activity Regulates Cysteine Homeostasis in Arabidopsis
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 656–669, https://doi.org/10.1104/pp.109.147975
Expression of Rapeseed Microsomal Lysophosphatidic Acid Acyltransferase Isozymes Enhances Seed Oil Content in Arabidopsis
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 670–684, https://doi.org/10.1104/pp.109.148247
A Putative Phosphatase, LSF1, Is Required for Normal Starch Turnover in Arabidopsis Leaves
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 685–697, https://doi.org/10.1104/pp.109.148981
Increasing Sucrose Uptake Capacity of Wheat Grains Stimulates Storage Protein Synthesis
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 698–710, https://doi.org/10.1104/pp.109.150854
The Laforin-Like Dual-Specificity Phosphatase SEX4 from Arabidopsis Hydrolyzes Both C6- and C3-Phosphate Esters Introduced by Starch-Related Dikinases and Thereby Affects Phase Transition of α-Glucans
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 711–722, https://doi.org/10.1104/pp.109.149914
Studies of the Kinetic Mechanism of Maize Endosperm ADP-Glucose Pyrophosphorylase Uncovered Complex Regulatory Properties
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 1056–1064, https://doi.org/10.1104/pp.109.149450
BIOENERGETICS AND PHOTOSYNTHESIS
Thylakoid Protein Phosphorylation in Higher Plant Chloroplasts Optimizes Electron Transfer under Fluctuating Light
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 723–735, https://doi.org/10.1104/pp.109.150250
Oscillatory Growth in Lily Pollen Tubes Does Not Require Aerobic Energy Metabolism
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 736–746, https://doi.org/10.1104/pp.109.150896
Divalent Metal Ions in Plant Mitochondria and Their Role in Interactions with Proteins and Oxidative Stress-Induced Damage to Respiratory Function
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 747–761, https://doi.org/10.1104/pp.109.147942
Stimulation of Nonselective Amino Acid Export by Glutamine Dumper Proteins
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 762–773, https://doi.org/10.1104/pp.109.151746
CELL BIOLOGY AND SIGNAL TRANSDUCTION
WallGen, Software to Construct Layered Cellulose-Hemicellulose Networks and Predict Their Small Deformation Mechanics
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 774–786, https://doi.org/10.1104/pp.109.146936
Real-Time Imaging of Cellulose Reorientation during Cell Wall Expansion in Arabidopsis Roots
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 787–796, https://doi.org/10.1104/pp.109.150128
Flexibility contra Stiffness: The Phragmoplast as a Physical Barrier for Beads But Not for Vesicles
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 1065–1072, https://doi.org/10.1104/pp.109.150417
Apyrase (Nucleoside Triphosphate-Diphosphohydrolase) and Extracellular Nucleotides Regulate Cotton Fiber Elongation in Cultured Ovules
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 1073–1083, https://doi.org/10.1104/pp.109.147637
DEVELOPMENT AND HORMONE ACTION
The REDUCED LEAFLET Genes Encode Key Components of the trans-Acting Small Interfering RNA Pathway and Regulate Compound Leaf and Flower Development in Lotus japonicus
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 797–807, https://doi.org/10.1104/pp.109.140947
The Role of Casein Kinase II in Flowering Time Regulation Has Diversified during Evolution
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 808–820, https://doi.org/10.1104/pp.109.148908
SEUSS and SEUSS-LIKE Transcriptional Adaptors Regulate Floral and Embryonic Development in Arabidopsis
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 821–836, https://doi.org/10.1104/pp.109.146183
Characterization of the Possible Roles for B Class MADS Box Genes in Regulation of Perianth Formation in Orchid
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 837–853, https://doi.org/10.1104/pp.109.147116
ENVIRONMENTAL STRESS AND ADAPTATION TO STRESS
Biochemical and Molecular Characterization of PvPAP3, a Novel Purple Acid Phosphatase Isolated from Common Bean Enhancing Extracellular ATP Utilization
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 854–865, https://doi.org/10.1104/pp.109.147918
Arabidopsis Deadenylases AtCAF1a and AtCAF1b Play Overlapping and Distinct Roles in Mediating Environmental Stress Responses
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 866–875, https://doi.org/10.1104/pp.109.149005
A Raf-Like MAPKKK Gene DSM1 Mediates Drought Resistance through Reactive Oxygen Species Scavenging in Rice
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 876–890, https://doi.org/10.1104/pp.109.149856
Enhanced Abscisic Acid-Mediated Responses in nia1nia2noa1-2 Triple Mutant Impaired in NIA/NR- and AtNOA1-Dependent Nitric Oxide Biosynthesis in Arabidopsis
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 891–903, https://doi.org/10.1104/pp.109.148023
Chitinase-Like Protein CTL1 Plays a Role in Altering Root System Architecture in Response to Multiple Environmental Conditions
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 904–917, https://doi.org/10.1104/pp.109.149849
Gravity-Induced Modifications to Development in Hypocotyls of Arabidopsis Tubulin Mutants
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 918–926, https://doi.org/10.1104/pp.109.147330
GENETICS, GENOMICS, AND MOLECULAR EVOLUTION
Aneuploidy Causes Tissue-Specific Qualitative Changes in Global Gene Expression Patterns in Maize
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 927–938, https://doi.org/10.1104/pp.109.150466
MEF9, an E-Subclass Pentatricopeptide Repeat Protein, Is Required for an RNA Editing Event in the nad7 Transcript in Mitochondria of Arabidopsis
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 939–947, https://doi.org/10.1104/pp.109.151175
PLANTS INTERACTING WITH OTHER ORGANISMS
The Pepper 9-Lipoxygenase Gene CaLOX1 Functions in Defense and Cell Death Responses to Microbial Pathogens
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 948–967, https://doi.org/10.1104/pp.109.147827
Arabidopsis Spermidine Synthase Is Targeted by an Effector Protein of the Cyst Nematode Heterodera schachtii
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 968–984, https://doi.org/10.1104/pp.109.150557
Reactive Oxygen Species Are Involved in Plant Defense against a Gall Midge
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 985–999, https://doi.org/10.1104/pp.109.150656
Knockdown of the Symbiotic Sucrose Synthase MtSucS1 Affects Arbuscule Maturation and Maintenance in Mycorrhizal Roots of Medicago truncatula
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 1000–1014, https://doi.org/10.1104/pp.109.149898
Novel Bifunctional Nucleases, OmBBD and AtBBD1, Are Involved in Abscisic Acid-Mediated Callose Deposition in Arabidopsis
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 1015–1029, https://doi.org/10.1104/pp.109.147645
Jasmonate-Dependent and -Independent Pathways Mediate Specific Effects of Solar Ultraviolet B Radiation on Leaf Phenolics and Antiherbivore Defense
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 1084–1095, https://doi.org/10.1104/pp.109.148999
WHOLE PLANT AND ECOPHYSIOLOGY
Tracing Cationic Nutrients from Xylem into Stem Tissue of French Bean by Stable Isotope Tracers and Cryo-Secondary Ion Mass Spectrometry
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 1030–1043, https://doi.org/10.1104/pp.109.143776
SYSTEMS BIOLOGY, MOLECULAR BIOLOGY, AND GENE REGULATION
Functional Characterization of Poplar Wood-Associated NAC Domain Transcription Factors
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 1044–1055, https://doi.org/10.1104/pp.109.148270
A Sugar-Inducible Protein Kinase, VvSK1, Regulates Hexose Transport and Sugar Accumulation in Grapevine Cells
Plant Physiology, Volume 152, Issue 2, February 2010, Pages 1096–1106, https://doi.org/10.1104/pp.109.149138
