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LARGE-SCALE BIOLOGY ARTICLES
Tissue-Specific Profiling Reveals Transcriptome Alterations in Arabidopsis Mutants Lacking Morphological PhenotypesMost loss-of-function single mutants show no visible phenotype differences compared with the wild type. This work shows that mutations in duplicate transcription factor genes of the root epidermis elicit dramatic changes in transcript profiles despite the lack of a morphological defect, illustrating the importance of in-depth phenotypic analyses and the complexity of duplicate gene diversification.
COPPER RESPONSE REGULATOR1–Dependent and –Independent Responses of the Chlamydomonas reinhardtii Transcriptome to Dark AnoxiaThis work examines the transcriptomic responses of Chlamydomonas to the combined conditions of anoxia and darkness, finding that the cells implement acclimation strategies to save and generate energy using all available resources and that COPPER RESPONSE REGULATOR1, a transcription factor involved in signaling in hypoxia and copper deficiency, plays an important role in these responses.
Dynamic Expression of Imprinted Genes Associates with Maternally Controlled Nutrient Allocation during Maize Endosperm DevelopmentGenomic imprinting refers to the differential expression of parental alleles in a parent-of-origin manner. Through a genome-wide identification of the imprinted genes in hybrid maize endosperm, this work provides evidence that the allele-specific expression status of the most imprinted genes is subject to dynamic change associated with different developmental events in the maize endosperm.
Establishing a Framework for the Ad/Abaxial Regulatory Network of Arabidopsis: Ascertaining Targets of Class III HOMEODOMAIN LEUCINE ZIPPER and KANADI RegulationHD-ZIPIII proteins and KANADI proteins are responsible for tailoring transcription in cells that will make up different parts of the leaf and in the self-renewing stem cells. This article reports which genes are turned on and off by the HD-ZIPIII and KANADI proteins and, therefore, how these proteins act to regulate the growth of new leaves and branches.
RESEARCH ARTICLES
TED, an Autonomous and Rare Maize Transposon of the Mutator Superfamily with a High Gametophytic Excision FrequencyThis work identifies TED, an autonomous maize transposable element related to the well-studied MuDR Mutator elements, but with some differences, including low copy number and a strong tendency to excise during the mitotic divisions of the gametophyte.
Expression Quantitative Trait Locus Mapping across Water Availability Environments Reveals Contrasting Associations with Genomic Features in ArabidopsisExpression quantitative trait locus mapping in well-watered and drying soil revealed differential gene expression resulting from standing genetic variation, environmental condition, and gene × environment interactions. Genomic features were then shown to be predictive of genetic and environmental variation in gene expression, but in contrasting ways.
The More the Merrier: Recent Hybridization and Polyploidy in CardamineAllopolyploids usually arise by hybridization of two species. This work examines the evolutionary role of a triploid bitter-cress hybrid (Cardamine × insueta) in the origin of trigenome hybrids (Cardamine × schulzii) and elucidates the 110-year history of interspecies hybridization in Cardamine, demonstrating that semifertile triploid hybrids may facilitate the origin of new trigenome allopolyploids.
The Fragaria vesca Homolog of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 Represses Flowering and Promotes Vegetative GrowthThis work reveals that the woodland strawberry ortholog of the floral activator SOC1 (Fv SOC1) is the general regulator of the photoperiodic development in this perennial short-day plant. It suppresses photoperiodic flowering by activating a major floral repressor Fv TFL1 and mediates photoperiodic signaling to promote runner development through regulating gibberellin biosynthetic genes.
ETHYLENE-INSENSITIVE3 Is a Senescence-Associated Gene That Accelerates Age-Dependent Leaf Senescence by Directly Repressing miR164 Transcription in ArabidopsisThis work demonstrates that EIN3 is a functional senescence-associated gene and defines a continuation of the signaling pathway involving EIN2-EIN3-miR164-NAC2 in regulating leaf senescence. The findings provide a mechanistic insight into how ethylene promotes the progression of leaf senescence in Arabidopsis.
A Kinetic Analysis of the Auxin Transcriptome Reveals Cell Wall Remodeling Proteins That Modulate Lateral Root Development in ArabidopsisWe identified genes involved in auxin-dependent lateral root formation using high temporal resolution and genome-wide transcript abundance analysis of auxin-treated Arabidopsis roots. Cell wall modification mutants, revealed by a reverse-genetic screen, had root phenotypes, supporting the hypothesis that auxin-mediated cell wall remodeling is an essential feature of lateral root development.
The Ubiquitin Receptor DA1 Interacts with the E3 Ubiquitin Ligase DA2 to Regulate Seed and Organ Size in ArabidopsisAlthough size control is a fundamental question in developmental biology, little is known about the mechanisms that determine seed and organ size in plants. Here, we show that two ubiquitin-related proteins, DA1 and DA2, interact genetically and physically with each other to regulate seed and organ size in Arabidopsis, suggesting that DA1 and DA2 are promising targets for crop improvement.
An-1 Encodes a Basic Helix-Loop-Helix Protein That Regulates Awn Development, Grain Size, and Grain Number in RiceAn-1 regulates the formation of long awns of seeds, which are important for seed dispersal in wild rice. However, An-1 has been selected in cultivated rice, which leads to loss of awn as well as more grains per panicle and higher yield per plant. Cloning of An-1 provides insight into how artificial selection shaped plant morphology to meet human demands during the long history of domestication.
The BRASSINOSTEROID INSENSITIVE1–LIKE3 Signalosome Complex Regulates Arabidopsis Root DevelopmentBrassinosteroids are essential regulators of plant growth and development. While BRI1 signaling regulates cellular growth in the majority of plant tissues, our study uncovers the composition of the BRL3 receptor complex in Arabidopsis and addresses cell type–specific roles for BRL3 signaling in root development.
Arabidopsis KINETOCHORE NULL2 Is an Upstream Component for Centromeric Histone H3 Variant cenH3 Deposition at CentromeresThis work finds that Arabidopsis KINETOCHORE NULL2 (KNL2) colocalizes with the centromere histone variant cenH3. Characterization of knl2 mutants showed reduction of cenH3 deposition at centromeres, abnormalities of mitosis and meiosis, seed abortion, and alterations in DNA methylation.
Arabidopsis ACTIN-DEPOLYMERIZING FACTOR7 Severs Actin Filaments and Regulates Actin Cable Turnover to Promote Normal Pollen Tube GrowthPollen tube growth is highly dependent on dynamic remodeling of the actin cytoskeleton, but the mechanisms that regulate the dynamic turnover of longitudinal actin cables in pollen tubes remain largely unknown. Here, we show that ACTIN-DEPOLYMERIZING FACTOR7 inhibits nucleotide exchange on actin and severs filaments in pollen tubes, thereby promoting turnover of longitudinal actin cables.
Cellular Auxin Homeostasis under High Temperature Is Regulated through a SORTING NEXIN1–Dependent Endosomal Trafficking PathwayThis work provides a mechanistic explanation linking increased auxin level and plant development under high temperature and comprehensively demonstrates that intracellular auxin homeostasis is a critical factor in plant adaptation to high temperature.
The Endoplasmic Reticulum Is the Main Membrane Source for Biogenesis of the Lytic Vacuole in ArabidopsisThis work uses genetic and pharmacological interference in combination with live-cell imaging, three-dimensional reconstruction, and electron microscopy to monitor trafficking to the tonoplast of the two proton pumps, V-ATPase and V-PPase. The results provide strong evidence for a Golgi-independent route of vacuolar biogenesis in plant cells.
A Membrane-Bound NAC Transcription Factor, ANAC017, Mediates Mitochondrial Retrograde Signaling in ArabidopsisThis work identifies a biological role for ANAC017 as an integral cellular component in mitochondrial retrograde signaling and a high-level transcriptional regulator that is necessary for H2O2-mediated primary stress responses in plants.
The Membrane-Bound NAC Transcription Factor ANAC013 Functions in Mitochondrial Retrograde Regulation of the Oxidative Stress Response in ArabidopsisThis work reports the discovery of a cis-regulatory motif in the promoters of genes that are subject to mitochondrial retrograde regulation and the identification of transcription factors that bind to this element, thereby steering mitochondrial retrograde-induced gene expression.
Histone Deacetylase Complex1 Expression Level Titrates Plant Growth and Abscisic Acid Sensitivity in ArabidopsisChemical modification of histones alters DNA structure and regulates gene expression. We have identified the Histone Deacetylase Complex (HDC) 1 protein as a component of chromatin in plants required for histone deacetylation and for induction of stress-inducible genes. HDC1-overexpression improves germination and plant growth without affecting plant morphology.
Dual Role for Phospholipid:Diacylglycerol Acyltransferase: Enhancing Fatty Acid Synthesis and Diverting Fatty Acids from Membrane Lipids to Triacylglycerol in Arabidopsis LeavesThis work finds that Arabidopsis PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE1 (PDAT1) is a critical enzyme in triacylglycerol assembly in vegetative tissues. Overexpression of PDAT1 enhances both fatty acid and triacylglycerol synthesis in leaves. The results suggest genetic engineering strategies to increase oil accumulation in biomass crops used for feed and for biofuel production.
Zeaxanthin Binds to Light-Harvesting Complex Stress-Related Protein to Enhance Nonphotochemical Quenching in Physcomitrella patensIn the moss Physcomitrella patens, LHCSR and PSBS, which trigger nonphotochemical quenching (NPQ) in green algae and vascular plants, respectively, are both active. This work reports that zeaxanthin, an NPQ enhancer, is far more active on LHCSR-dependent NPQ than on the PSBS-dependent NPQ. Consistent with this, zeaxanthin binds LHCSR in excess light.
An Arabidopsis Soil-Salinity–Tolerance Mutation Confers Ethylene-Mediated Enhancement of Sodium/Potassium HomeostasisThe soil salinity tolerance of an Arabidopsis mutant is shown to be caused by a mutation in the ETO1 gene that results in ethylene overproduction. Increased ethylene causes root stele reactive oxygen species (ROS)–dependent reductions in root Na influx and xylem loading and stelar ROS-independent enhancement of root K status, thus improving plant Na/K homeostasis and salinity tolerance.
Temporal-Spatial Interaction between Reactive Oxygen Species and Abscisic Acid Regulates Rapid Systemic Acclimation in PlantsAn autopropagating wave of reactive oxygen species (the ROS wave) rapidly spreads from a local tissue exposed to stress to the entire plant. In coordination with other systemic signals and abscisic acid, it activates systemic acclimation mechanisms in the entire plant and enhances tolerance to abiotic stress. The enhanced tolerance is specific to the original stress that induces it.
Repression of Growth Regulating Factors by the MicroRNA396 Inhibits Cell Proliferation by UV-B Radiation in Arabidopsis LeavesInhibition of leaf growth is one of the most consistent responses of plants upon exposure to UV-B radiation, and this radiation affects cell proliferation and cell expansion. In this work, we demonstrate that inhibition of cell proliferation by UV-B radiation in Arabidopsis is mediated by GROWTH-REGULATING FACTORs and the microRNA miR396 and that this pathway depends on the mitogen-activated protein kinase MPK3.
The C2H2 Transcription Factor REGULATOR OF SYMBIOSOME DIFFERENTIATION Represses Transcription of the Secretory Pathway Gene VAMP721a and Promotes Symbiosome Development in Medicago truncatulaThis work reports a plant transcription factor, RSD, that is required for symbiosome development and symbiotic nitrogen fixation (SNF) in the model legume Medicago truncatula. RSD represses the expression of the secretory pathway gene VAMP721a, which suggests that alteration in this pathway is important for SNF.
The Cytosolic Nucleoprotein of the Plant-Infecting Bunyavirus Tomato Spotted Wilt Recruits Endoplasmic Reticulum–Resident Proteins to Endoplasmic Reticulum Export SitesThis work identifies a major role for the cytosolic structural protein of plant-infecting bunyaviruses in the concentration of viral glycoprotein cargo at endoplasmic reticulum export sites before their traffic to the Golgi complex where they further mature.
The Tomato Fni3 Lysine-63–Specific Ubiquitin-Conjugating Enzyme and Suv Ubiquitin E2 Variant Positively Regulate Plant ImmunityThe Ubc13-type ubiquitin-conjugating enzyme catalyzes Lys-63–specific ubiquitination, which usually plays a nonproteolytic, regulatory role in the cell. In this study, Fni3, the tomato homolog of Ubc13, and its cofactor Suv were identified and shown to regulate Fen-mediated and other R protein–mediated, immunity-associated cell death, revealing an important mechanism for regulation of the plant immune system.
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