Table of Contents
IN BRIEF
LARGE-SCALE BIOLOGY ARTICLES
- Genome Comparison of Barley and Maize Smut Fungi Reveals Targeted Loss of RNA Silencing Components and Species-Specific Presence of Transposable Elements
The genome sequence of Ustilago hordei revealed that transposable elements were involved in restructuring of the genome, which affected fungal reproductive biology and evolution of genes encoding effector proteins. Comparison to other smuts indicated loss of genome defense components in Ustilago maydis and control of repetitive sequences by repeat-induced point mutation in U. hordei.
- Screening a cDNA Library for Protein–Protein Interactions Directly in Planta
This article presents a method to screen a plant cDNA library for genes encoding proteins that interact with a bait protein directly in plants using bimolecular fluorescence complementation technology. Proof-of-concept experiments identified both known and novel Arabidopsis thaliana proteins important for Agrobacterium-mediated plant transformation.
RESEARCH ARTICLES
- required to maintain repression2 Is a Novel Protein That Facilitates Locus-Specific Paramutation in Maize
This research identifies a previously unknown clade of plant-specific proteins whose founding member is shown to facilitate meiotically heritable trans-homologue repression in maize. The findings highlight a diversification of epigenomic control mechanisms in higher plants.
- Grass MicroRNA Gene Paleohistory Unveils New Insights into Gene Dosage Balance in Subgenome Partitioning after Whole-Genome Duplication
Reconstruction of the grass genome paleohistory revealed subgenome partitioning of microRNA (miRNA) genes during post-whole-genome duplication diploidization. The evolutionary scenario of miRNAs from the ancestral founder pool to the modern complements displayed dosage balance constrictions on the deletion/retention of miRNAs and associated target genes wherein transposable elements may play a major role in miRNA gene synteny disruption.
- Integrated Systems View on Networking by Hormones in Arabidopsis Immunity Reveals Multiple Crosstalk for Cytokinin
Predicting the system response to the invading pathogen, dynamic modeling of hormone disease networks explores the effect of cytokinin on immune defense. Together with validation experiments on disease phenotypes and monitoring hormonal responses and gene expression data, this work identified synergistic crosstalk for cytokinin and antagonism between auxin and cytokinin regarding immunity.
- DEXH Box RNA Helicase–Mediated Mitochondrial Reactive Oxygen Species Production in Arabidopsis Mediates Crosstalk between Abscisic Acid and Auxin Signaling
An Arabidopsis thaliana abscisic acid (ABA) overly sensitive mutant, abo6, was identified, and ABO6 was found to encode a DEXH box RNA helicase that regulates the splicing of genes of complex I in mitochondria. ABA and auxin signaling are shown to regulate primary root growth and seed germination via reactive oxygen species produced in mitochondria.
- Evolution of Double Positive Autoregulatory Feedback Loops in CYCLOIDEA2 Clade Genes Is Associated with the Origin of Floral Zygomorphy
This work examines the role of CYC2 clade genes in floral asymmetry in Primulina heterotricha, finding that CYC1C and CYC1D positively auto- and cross-regulate both themselves and each other in a double positive autoregulatory feedback loop, a regulatory mechanism that may be conserved in other clades with zygomorphic flowers.
- Inflorescence Meristem Identity in Rice Is Specified by Overlapping Functions of Three AP1/FUL-Like MADS Box Genes and PAP2, a SEPALLATA MADS Box Gene
This work examines the reproductive phase transition in rice using laser microdissection and microarrays in addition to biochemical and genetic approaches. The results support that PAP2, a MADS box gene belonging to a grass-specific subclade of the SEP subfamily, and three AP1/FUL-like genes coordinately act in the meristem to specify the identity of the inflorescence meristem downstream of the florigen signal.
- Activation of the Carbon Concentrating Mechanism by CO2 Deprivation Coincides with Massive Transcriptional Restructuring in Chlamydomonas reinhardtii
The CO2-concentrating mechanism (CCM) is key to allowing robust growth of eukaryotic algae. CCM activation by exposure of cells to low CO2 accompanies induction of genes involved in inorganic carbon uptake and concomitant suppression of many metabolism-related genes. Transcriptome and promoter motif analyses provide insights into CCM-associated regulatory networks.
- Transcriptome-Wide Changes in Chlamydomonas reinhardtii Gene Expression Regulated by Carbon Dioxide and the CO2-Concentrating Mechanism Regulator CIA5/CCM1
Using powerful tools to investigate the regulation of global gene expression in the model microalga Chlamydomonas reinhardtii, we observed an impact of CO2 and CIA5, a key transcription regulator, on expression of almost 25% of all the genes. We also discovered an array of gene clusters with distinctive expression patterns that provide insight into the regulatory interaction between CIA5 and CO2.
- A Chloroplast Light-Regulated Oxidative Sensor for Moderate Light Intensity in Arabidopsis
This study identifies a regulatory oxidative pathway, comprised of thioredoxin and peroxiredoxin, in Arabidopsis thaliana chloroplasts. It shows that the pathway is used to sense photosynthetic peroxide formation under low to moderate light intensity and proposes that the oxidative signal adjusts the photosynthetic linear electron flow to fluctuating environmental conditions.
- Phosphorylation of FAR-RED ELONGATED HYPOCOTYL1 Is a Key Mechanism Defining Signaling Dynamics of Phytochrome A under Red and Far-Red Light in Arabidopsis
When young plants emerge from the soil or canopy into direct sunlight, they must rapidly adapt to the new light environment containing a higher ratio of red/far-red light. This work reveals the molecular mechanism of how the photoreceptor phyA differentially transduces red and far-red light signals to light-responsive genes for better plant survival in natural environments.
- Photosynthetic Quantum Yield Dynamics: From Photosystems to Leaves
The quantum yield for CO2 fixation is wavelength dependent due to (1) light absorption by nonphotosynthetic pigments, (2) inefficient energy transfer, and (3) the excitation balance between the two photosystems. The growth-light spectrum alters the excitation balance by altering the photosystem composition, as shown both in vivo and in vitro. Enhancement effects can increase the quantum yield.
- Assembly of Synthetic Locked Phycocyanobilin Derivatives with Phytochrome in Vitro and in Vivo in Ceratodon purpureus and Arabidopsis
This article shows that two synthetic “locked” chromophores, termed 15ZaPCB and 15EaPCB, are incorporated into recombinant phytochrome and that feeding of 15EaPCB to the moss Ceratodon purpureus and the seed plant Arabidopsis thaliana results in an onset of phytochrome effects in darkness. Thus, the 15EaPCB phytochrome adduct mimics Pfr, the physiologically active form of phytochrome.
- Operon flv4-flv2 Provides Cyanobacterial Photosystem II with Flexibility of Electron Transfer
This work shows that the flv4-flv2 operon provides many β-cyanobacteria with a so far unknown photoprotection mechanism that evolved in parallel with oxygen-evolving photosystem II
- The Essential Role of the N-Terminal Domain of the Orange Carotenoid Protein in Cyanobacterial Photoprotection: Importance of a Positive Charge for Phycobilisome Binding
This article provides information about the interaction between the phycobilisomes and the Orange Carotenoid Protein needed for photoprotection. Its red light–activated form has an open structure that allows the interaction of its N-terminal domain, containing the Arg155, with the phycobilisome, permitting a closer interaction between the carotenoid and the phycobilisome chromophores.
- Transposase-Derived Proteins FHY3/FAR1 Interact with PHYTOCHROME-INTERACTING FACTOR1 to Regulate Chlorophyll Biosynthesis by Modulating HEMB1 during Deetiolation in Arabidopsis
This study identifies FHY3 and FAR1 as positive regulators directly affecting chlorophyll biosynthesis through the activation of HEMB1. It shows that FHY3 protein physically interacts with PIF1, a negative regulator in the pathway, and they work coordinately to modulate the plant greening process.
- Fatty Acid Phytyl Ester Synthesis in Chloroplasts of Arabidopsis
This work identifies two phytyl ester synthases that act in fatty acid phytyl ester synthesis in chloroplasts during senescence and nitrogen deprivation to maintain the integrity of the photosynthetic membrane during abiotic stress and senescence.
- Contribution of CoA Ligases to Benzenoid Biosynthesis in Petunia Flowers
Biochemical and genetic characterization of two petunia CoA ligases reveals that subcellular compartmentalization of enzymes determines their involvement in the benzenoid metabolic network. Additional evidence shows that formation of cinnamoyl-CoA in peroxisomes is the committed step in the synthesis of benzoyl-CoA via the β-oxidative pathway.
- The ARP2/3 Complex Mediates Guard Cell Actin Reorganization and Stomatal Movement in Arabidopsis
This study reports the isolation of hsr3, an allele of the Arabidopsis ARPC2 locus encoding a subunit of the ARP2/3 complex involved in the regulation of the actin cytoskeleton. In hsr3, reduced abscisic acid–induced stomatal closure is associated with failure of actin reassembly, indicating that modulation of the cytoskeleton through the ARP2/3 complex is crucial for stomatal regulation.
- Plant Vegetative and Animal Cytoplasmic Actins Share Functional Competence for Spatial Development with Protists
This study shows that the vegetative class of plant actins and the cytoplasmic class of animal actins share conserved functions that were inherited from an ancestral protist actin sequence. Thus, some single-celled protists contain actin that can perform the complex processes required for multicellular development.
- The Recombinases DMC1 and RAD51 Are Functionally and Spatially Separated during Meiosis in Arabidopsis
This article presents evidence, obtained in Arabidopsis thaliana, that two central DNA repair proteins, the recombinases DMC1 and RAD51, are spatially and functionally separated, respectively, during meiotic DNA repair and shows that a well-known DNA damage response factor, the ATR kinase, is involved in regulating DMC1 deposition.
- Arabidopsis Microtubule-Associated Protein MAP65-3 Cross-Links Antiparallel Microtubules toward Their Plus Ends in the Phragmoplast via Its Distinct C-Terminal Microtubule Binding Domain
MAP65-3 contains a distinct C-terminal microtubule binding site that is not shared by other Arabidopsis MAP-65 proteins. This study demonstrates that this C-terminal extension determines the protein’s specific function in cross-linking antiparallel microtubules in the phragmoplast midzone.
- The Golgi-Localized Arabidopsis Endomembrane Protein12 Contains Both Endoplasmic Reticulum Export and Golgi Retention Signals at Its C Terminus
A Golgi-localized polytopic integral membrane protein, EMP12, was shown to contain an endoplasmic reticulum export signal (FVY) and a Golgi retention signal (KXE/D) that interact with COPII and COPI subunits, respectively, in Arabidopsis cells. These sorting signals are highly conserved in all plant EMP isoforms and, thus, likely represent a general mechanism for EMP targeting in plant cells.
- A Membrane Microdomain-Associated Protein, Arabidopsis Flot1, Is Involved in a Clathrin-Independent Endocytic Pathway and Is Required for Seedling Development
This work reveals that Flot1 functions in Arabidopsis thaliana seedling development and is involved in a membrane microdomain-dependent, but clathrin-independent, endocytic pathway. Moreover, the dynamic behavior of Flot1-positive puncta differs considerably from that of clathrin light chain–positive puncta.
- The Sg-1 Glycosyltransferase Locus Regulates Structural Diversity of Triterpenoid Saponins of Soybean
Group A saponins in soybean are diversified compounds belonging to a group of triterpene saponins and are causal components for bitterness and astringent aftertastes of soy products. This work describes the identification of Sg-1, a UDP-sugar–dependent glycosyltransferase gene that is responsible for the unpleasant tastes due to allelic variation regulating the terminal sugar species in group A saponins.
- Characterization of Arabidopsis NEET Reveals an Ancient Role for NEET Proteins in Iron Metabolism
This work describes biochemical, biophysical, structural, and genetic analyses of an Arabidopsis homolog of mammalian NEET proteins, which are involved in a wide range of cellular processes. It finds that At-NEET plays a key role in plant development, senescence, reactive oxygen species homeostasis, and iron metabolism.
- Nramp5 Is a Major Transporter Responsible for Manganese and Cadmium Uptake in Rice
Rice accumulates high concentrations of Mn. The high uptake of Mn in rice is mediated by a member of Nramp proteins, which is polarly localized at the plasma membrane of both the exodermis and endodermis cells in the roots. This protein also functions as a major transporter of Cd.
- PHO2-Dependent Degradation of PHO1 Modulates Phosphate Homeostasis in Arabidopsis
PHO2, a ubiquitin-conjugating E2 enzyme, maintains phosphate homeostasis by regulating phosphate uptake and translocation. This work identifies PHO1, a membrane-spanning protein implicated in xylem loading of phosphate, as a PHO2-interacting protein in the endomembrane system and shows that PHO1 degradation is PHO2 dependent and involves multivesicular body–mediated vacuolar proteolysis.
- A Vacuolar β-Glucosidase Homolog That Possesses Glucose-Conjugated Abscisic Acid Hydrolyzing Activity Plays an Important Role in Osmotic Stress Responses in Arabidopsis
This work presents evidence for a novel abscisic acid production pathway involving At-BG2, a β-glucosidase, in the vacuole. This result suggests that abscisic acid is produced in multiple places by multiple pathways in response to abiotic stress.
- Cytosolic Glyceraldehyde-3-Phosphate Dehydrogenases Interact with Phospholipase Dδ to Transduce Hydrogen Peroxide Signals in the Arabidopsis Response to Stress
Plants produce hydrogen peroxide (H2O2) as a stress signal. This study shows that H2O2 promotes the binding of cytosolic, glycolytic enzymes, GAPCs, to the plasma membrane–associated phospholipase PLDδ. The GAPC–PLDδ interaction mediates the plant response to H2O2 and provides a molecular link between stress signaling and the alteration of cellular metabolism and growth in the plant response to drought.
- Chimeric FLS2 Receptors Reveal the Basis for Differential Flagellin Perception in Arabidopsis and Tomato
Arabidopsis cells expressing either the FLS2 ortholog from Arabidopsis or tomato specifically respond to picomolar concentrations of the flg22 ligand. However, these orthologs exhibit characteristic differences when challenged with flg22 variants. Hybrid forms made from both orthologs allowed attribution of these differences to distinct subsets within the 28 Leucine-rich repeats of their ectodomains.
- The MEKK1-MKK1/MKK2-MPK4 Kinase Cascade Negatively Regulates Immunity Mediated by a Mitogen-Activated Protein Kinase Kinase Kinase in Arabidopsis
Mitogen-activated protein kinase kinase kinase MEKK2 functions as a positive regulator of plant immunity mediated by the nucleotide binding–Leu-rich repeat Resistance protein SUMM2. MEKK2 interacts with MPK4 and is negatively regulated by the MEKK1-MKK1/MKK2-MPK4 kinase cascade.
