Table of Contents
IN BRIEF
LARGE-SCALE BIOLOGY ARTICLES
Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence AnalysisThe authors used comparative sequence analysis to delineate, using 12 flowering plants, conserved noncoding sequences in Arabidopsis thaliana and demonstrated a high enrichment for functional cis-regulatory elements in these conserved regions. Based on known binding sites, a gene regulatory network was generated, revealing new and condition-specific functional gene regulatory interactions.
Paired-End Analysis of Transcription Start Sites in Arabidopsis Reveals Plant-Specific Promoter SignaturesThis work presents a genome-scale data set that precisely identifies transcription start sites for a majority of Arabidopsis genes, revealing that plant promoters are not primarily TATA based and have an unexpected structure composed of many position-specific sequence elements. This analysis identifies combinations of factors that are likely to lead to transcription initiation.
RESEARCH ARTICLES
Evolution of the BBAA Component of Bread Wheat during Its History at the Allohexaploid LevelThe extracted tetraploid wheat (ETW) containing the BBAA subgenomes of hexaploid bread wheat has a stabilized karyotype but anomalous phenotypes. Genome-wide comparisons between ETW and natural tetraploid wheat revealed a large number of differentially expressed genes in ETW; these changes showed early occurrence and evolutionary persistence during bread wheat evolution.
Polyploid Evolution of the Brassicaceae during the Cenozoic EraThis study identified multiple whole-genome duplication (WGD) events among Brassicaceae species. Remarkably, these events, as well as previously identified WGD events, are synchronized in age, coincident with epoch transitions, adding to the evidence suggesting the environmental instability associated with these transitions favors polyploidy and rapid species diversification.
Integrated Syntenic and Phylogenomic Analyses Reveal an Ancient Genome Duplication in MonocotsWhole-genome duplication (WGD) is a primary source of genetic material for evolutionary variation. This work compares the genomes of four monocots and two eudicots using integrated phylogenomic and syntenic analyses, revealing an ancient WGD that shaped the genomes of all commelinid monocots, including grasses, bromeliads, bananas, gingers, palms, and other economically important plants.
DNA Topoisomerase I Affects Polycomb Group Protein-Mediated Epigenetic Regulation and Plant Development by Altering Nucleosome Distribution in ArabidopsisGiven the role of topoisomerases in relieving torsional stresses in DNA during replication or transcription, it is surprising that the topoisomerase TOP1α plays a role in specific developmental processes. This study uncovers a connection between TOP1α and the deposition of the histone H3K27me3 mark at Polycomb Group target genes, which regulates target gene expression and, hence, developmental events.
Genetical and Comparative Genomics of Brassica under Altered Ca Supply Identifies Arabidopsis Ca-Transporter OrthologsThis work uses multiple-environment expression quantitative trait locus analysis of the Brassica rapa genome, combined with comparative genomics of Arabidopsis, to identify putative vacuolar calcium transporters with potential uses in biofortification to increase the accumulation of calcium in food crops.
Dt2 Is a Gain-of-Function MADS-Domain Factor Gene That Specifies Semideterminacy in SoybeanThis work describes mapped-based cloning and characterization of a gain-of-function mutation (Dt2) that specifies semideterminate stem termination in soybean. Dt2 represents an evolutionary novelty and uniqueness of the genetic mechanisms underlying plant stem growth habit and may be a more productive alternative for soybean production, particularly in high fertility and irrigated environments.
LNK1 and LNK2 Are Transcriptional Coactivators in the Arabidopsis Circadian OscillatorThe plant circadian clock consists of multiple interlocked transcriptional feedback loops. This work shows that LNK1 and LNK2, two NIGHT LIGHT–INDUCIBLE AND CLOCK-REGULATED genes, encode transcriptional coactivators that physically interact in the nucleus with multiple Myb transcription factors (CCA1, LHY, RVE4, and RVE8) and are necessary for full transcriptional induction of PRR5 and TOC1 by RVE8.
HUA ENHANCER1 Is Involved in Posttranscriptional Regulation of Positive and Negative Regulators in Arabidopsis PhotomorphogenesisThis work reports that the expression of HEN1, a small regulatory RNA methyltransferase essential for microRNA biogenesis, is activated by light signaling pathways to regulate Arabidopsis photomorphogenesis. The expression of positive (HY5) and negative (TCPs) regulators is tuned by miR157d and miR319, respectively, in deetiolating seedlings, demonstrating a posttranscriptional control in the photomorphogenic development.
Transcriptome Analysis Reveals the Same 17 S-Locus F-Box Genes in Two Haplotypes of the Self-Incompatibility Locus of Petunia inflataThis work characterizes the pollen transcriptomes of Petunia inflata to identify all S-locus F-box (SLF) genes of two S-haplotypes, S2 and S3. In addition to the 10 previously identified SLF genes, the same seven novel SLF genes were identified in the two haplotypes, suggesting that a total of 17 SLF genes in these two haplotypes collectively regulate pollen specificity in self-incompatibility.
TAA1-Regulated Local Auxin Biosynthesis in the Root-Apex Transition Zone Mediates the Aluminum-Induced Inhibition of Root Growth in ArabidopsisAl toxicity is a major constraint to crop production in acidic soil worldwide. This study elucidates how Al may regulate root growth inhibition through mediating local auxin biosynthesis and signaling in the root-apex transition zone and provides insights into how environmental cues affect root growth plasticity through influencing local auxin biosynthesis and signaling.
Arabidopsis DELLA and Two HD-ZIP Transcription Factors Regulate GA Signaling in the Epidermis through the L1 Box cis-ElementThis work analyzes gene regulatory networks involved in GA responses by focusing on a lipase gene (LIP1) expressed in the epidermis during germination. The results support a model in which GA mediates the activation of downstream target genes containing L1 box sequences in their promoters by releasing two HD-ZIP TFs (ATML1 and PDF2) from their inhibitory interaction with DELLA proteins.
DELLAs Function as Coactivators of GAI-ASSOCIATED FACTOR1 in Regulation of Gibberellin Homeostasis and Signaling in ArabidopsisThis work reports the discovery of the DELLA-binding transcription factor GAF1 and shows that DELLAs and TPR act as coactivators and a corepressor with GAF1, respectively. GA converts the GAF1 complex from transcriptional activator to repressor via degradation of DELLAs. Accordingly, DELLAs turn on or off two sets of GA-regulated genes by dual functions, namely titration and coactivation.
The Cysteine Protease CEP1, a Key Executor Involved in Tapetal Programmed Cell Death, Regulates Pollen Development in ArabidopsisArabidopsis thaliana papain-like cysteine protease, CEP1, is a crucial executor that participates directly in tapetal cell wall hydrolysis and secretory structure formation during tapetal cell programmed cell death. Correct expression of CEP1 in the tapetum is necessary for timely tapetal cell degeneration and functional pollen formation.
The Boron Efflux Transporter ROTTEN EAR Is Required for Maize Inflorescence Development and FertilityThis work reports the isolation and characterization of a mutant called rotten ear (rte), which shows growth and fertility defects in maize inflorescences. rte is required for the uptake and transport of the micronutrient boron and is necessary for the structural integrity of maize cell walls.
Transport of Boron by the tassel-less1 Aquaporin Is Critical for Vegetative and Reproductive Development in MaizeIdentification and analysis of the maize boron (B) transporter mutant tassel-less1 demonstrated that the primary symptoms of B deficiency are defects in vegetative and reproductive meristems, thus providing an explanation for the reductions in yield observed under B-limited conditions.
The Structure of the Catalytic Domain of a Plant Cellulose Synthase and Its Assembly into DimersSmall-angle x-ray scattering gives a glimpse at the solution structure of the catalytic domains of plant cellulose synthase and their dimerization. Dimerization through the plant-specific sequences of the catalytic domain provides important clues for how Zn-finger domains couple these fundamental scaffold units into large, multimeric synthase complexes.
Arabidopsis and Maize RidA Proteins Preempt Reactive Enamine/Imine Damage to Branched-Chain Amino Acid Biosynthesis in PlastidsPlant RidA proteins protect an enzyme of branched-chain amino acid biosynthesis from inactivation by hydrolyzing reactive pathway intermediates before they can damage the enzyme. RidA proteins are thus crucial for the efficient biosynthesis of branched-chain amino acids in plants and provide an iconic example of the preemption of metabolite damage.
Cytosolic Phosphorylating Glyceraldehyde-3-Phosphate Dehydrogenases Affect Arabidopsis Cellular Metabolism and Promote Seed Oil AccumulationGenetic alterations of the cytosolic, phosphorylating glyceraldehyde-3-phosphate dehydrogenase, GAPC, have substantial impacts on the overall cellular production of reductants, energy, and carbohydrate metabolites as well as seed production. Increased GAPC expression contributes to enhanced seed oil accumulation.
Combined Increases in Mitochondrial Cooperation and Oxygen Photoreduction Compensate for Deficiency in Cyclic Electron Flow in Chlamydomonas reinhardtiiContribution of cyclic electron flow to photosynthesis and biomass productivity is explored in a Chlamydomonas reinhardtii PGRL1-deficient mutant. Induction of different mechanisms, including cooperation between photosynthesis and mitochondrial respiration and oxygen photoreduction (direct or flavodiiron-mediated), efficiently compensates for the deficit in ATP supply under steady state, but not under transient or fluctuating conditions.
Nanodomains of Cytochrome b6f and Photosystem II Complexes in Spinach Grana Thylakoid MembranesColocalization of cytochrome b6f and photosystem II complexes creates nanodomains that facilitate rapid exchange of the lipophilic electron carrier plastoquinone in the crowded thylakoid grana membrane.
Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in ArabidopsisThis work presents a model of the plant intracellular trafficking system developed by analyzing the subcellular localization of GNOM ARF-GEF, which is crucial for auxin transport-mediated plant development. The data show that GNOM is associated with Golgi body, rather than endosomes as previously believed, and redefine our notions about the identity and function of recycling endosomes in plants.
Direct Phosphorylation and Activation of a Mitogen-Activated Protein Kinase by a Calcium-Dependent Protein Kinase in RiceThis study reveals a novel mechanism that regulates the mitogen-activated protein kinase (MAPK) cascade by a calcium-dependent protein kinase (CDPK) in land plants. The finding provides insight into the crosstalk mechanism between the CDPK and MAPK pathways and identifies a role for this mechanism in stress signal transduction and plant immunity.
Uric Acid Accumulation in an Arabidopsis Urate Oxidase Mutant Impairs Seedling Establishment by Blocking Peroxisome MaintenanceArabidopsis seeds with a mutation in urate oxidase show a defect in germination, fail to develop the cotyledons, and exhibit partially blocked β-oxidation. These phenotypes result from the accumulation of uric acid and are suppressed by the additional mutation of xanthine dehydrogenase, which prevents uric acid accumulation. The data presented show that peroxisome maintenance is compromised by uric acid.
Phylobiochemical Characterization of Class-Ib Aspartate/Prephenate Aminotransferases Reveals Evolution of the Plant Arogenate Phenylalanine PathwayPlants use phenylalanine to produce abundant and diverse phenylpropanoid compounds, such as flavonoids, tannins, and lignin. Through phylogenetic, bioinformatic, and biochemical analyses of prephenate aminotransferase enzymes from deep taxonomic lineages, this study revealed unique evolutionary history and molecular changes of key enzymes responsible for phenylalanine biosynthesis in plants.
Arabidopsis MSL10 Has a Regulated Cell Death Signaling Activity That Is Separable from Its Mechanosensitive Ion Channel ActivityMscS-Like 10, a mechanosensitive ion channel from Arabidopsis, has two functions, each attributable to a different domain of the protein. The C-terminal domain, which is conserved among all MscS-Like ion channels, mediates tension-regulated ion flux. The plant-specific N-terminal domain is capable of inducing cell death, and its activity is negatively regulated by its phosphorylation.
Arabidopsis SNAREs SYP61 and SYP121 Coordinate the Trafficking of Plasma Membrane Aquaporin PIP2;7 to Modulate the Cell Membrane Water PermeabilityThis work shows that the post-Golgi trafficking of PIP2;7 involves an interaction with SYP61 and SYP121 and that SYP61 and SYP121 colocalize and are physically associated in a SNARE complex. These findings suggest that SNAREs, and possibly a SYP61/SYP121 SNARE complex, play an important role in the regulation of the transport of the plasma membrane aquaporin.
The Ubiquitous Distribution of Late Embryogenesis Abundant Proteins across Cell Compartments in Arabidopsis Offers Tailored Protection against Abiotic StressLEA proteins accumulate in plant seeds prior to maturation drying, and some have been shown to protect membranes from desiccation. This work demonstrates the subcellular distribution of each of 51 Arabidopsis LEA proteins and suggests protection against desiccation or cold stress is tailored for each cellular compartment.
Closely Related NAC Transcription Factors of Tomato Differentially Regulate Stomatal Closure and Reopening during Pathogen AttackThis work reports the distinct mechanisms of two homologous NAC proteins of tomato, JA2 and JA2L, in regulating Pseudomonas syringae pv tomato DC3000–induced stomatal movement. Whereas JA2 acts in abscisic acid (ABA)–mediated stomatal closure by promoting ABA biosynthesis, JA2L functions in jasmonate/coronatine–mediated stomatal reopening by suppressing salicylic acid accumulation.
Interaction of the Arabidopsis GTPase RabA4c with Its Effector PMR4 Results in Complete Penetration Resistance to Powdery MildewUnexpectedly, an Arabidopsis RabA family GTPase directly interacted with a pathogen-induced, plasma membrane-bound callose synthase in unchallenged epidermal leaf cells as well as in response to powdery mildew. Overexpression of this Rab GTPase induced enhanced early callose deposition at powdery mildew infection sites and complete penetration resistance to this biotrophic fungus.
RETRACTED: The Arabidopsis Malectin-Like Leucine-Rich Repeat Receptor-Like Kinase IOS1 Associates with the Pattern Recognition Receptors FLS2 and EFR and Is Critical for Priming of Pattern-Triggered ImmunityThis work describes the function of the RLK IOS1 in Arabidopsis immunity against bacteria. IOS1 is required for optimal function of the immune receptors FLS2 and EFR and β-aminobutyric acid-induced resistance and priming. IOS1 associates with FLS2, EFR, and BAK1 and controls the ligand-induced FLS2-BAK1 association.
