Table of Contents
IN BRIEF
REVIEWS
LARGE-SCALE BIOLOGY ARTICLES
Reticulate Evolution of the Rye GenomeSurvey sequences of rye chromosomes were integrated with a new transcript map and a comparative genomics model to linearly order 22,426 gene loci. The rye genome exhibits five consecutive rearrangements in comparison to barley. Sequence and phylogenetic analysis reveal characteristics of introgressive hybridization and reticulated evolution of the rye genome.
Translational Landscape of Photomorphogenic ArabidopsisThis work describes translational activity at single-nucleotide resolution in deetiolating Arabidopsis. Light selectively triggers the increase or decrease of ribosome density of specific transcripts. This work also reports the global effects of upstream open reading frames and microRNAs in negatively regulating the translation of annotated open reading frames in deetiolating Arabidopsis.
Mechanisms of Functional and Physical Genome Reduction in Photosynthetic and Nonphotosynthetic Parasitic Plants of the Broomrape FamilyThe authors report the structure of ten plastid genomes from hemi- and holoparasitic plants and their closest nonparasitic relative. Structural plastome reconfiguration is associated with obligate parasitism. The extent of genome reduction after the loss of photosynthesis is governed by dispensable genes’ proximity to essential genes and the position in operons or by alternative gene function.
Nonsense-Mediated Decay of Alternative Precursor mRNA Splicing Variants Is a Major Determinant of the Arabidopsis Steady State TranscriptomeAlternative precursor mRNA splicing represents a major mechanism to increase transcriptome diversity in higher eukaryotes. This work demonstrates that a substantial fraction of the alternative splicing variants from Arabidopsis thaliana is subject to turn over via the RNA quality-control mechanism nonsense-mediated decay, having important implications for the regulation of gene expression.
RESEARCH ARTICLES
Genome-Wide Binding Analysis of the Transcription Activator IDEAL PLANT ARCHITECTURE1 Reveals a Complex Network Regulating Rice Plant ArchitectureThis work shows that the key rice architecture regulator IPA1 binds to promoters of target genes directly or indirectly at a different motif by interacting with PCF1 and PCF2. Expression profiling and further characterization of these target genes reveal a complex genetic regulatory network orchestrated by IPA1, providing insight into the regulation of plant development.
Nighttime Sugar Starvation Orchestrates Gibberellin Biosynthesis and Plant Growth in ArabidopsisThis work demonstrates that plants integrate the efficiency of photosynthesis over a period of days and transduce that information into a daily rate of gibberellin synthesis. This enables a plant to match its growth rate to its environment without unnecessary short-term fluctuations.
HFR1 Sequesters PIF1 to Govern the Transcriptional Network Underlying Light-Initiated Seed Germination in ArabidopsisThis study identifies the LONG HYPOCOTYL IN FAR-RED1 (HFR1)– PHYTOCHROME-INTERACTING FACTOR 1 (PIF1) pair as the central transcriptional regulatory module for rapid light-initiated transcriptome changes in imbibed seeds. HFR1 interacts with PIF1 to prevent PIF1 from binding to DNA, promoting light-initiated germination. The functionally antagonistic HFR1–PIF1 pair constructs a fail-safe mechanism for fine-tuning seed germination under low-level illumination.
Flower Development under Drought Stress: Morphological and Transcriptomic Analyses Reveal Acute Responses and Long-Term Acclimation in ArabidopsisDrought dramatically affects plant reproductive development and crop yield, but previous research has primarily focused on vegetative development. This work uses a scheme that allows plant growth with limited water to study plant responses to drought during reproductive development. The authors examine floral developmental defects and identify key genes affecting this process.
Copy Number Variation in Transcriptionally Active Regions of Sexual and Apomictic Boechera Demonstrates Independently Derived Apomictic LineagesThis work compared the genomic signature of variable copy numbers of transcribed genes between sexual and asexual (apomictic) plants of the genus Boechera and showed that the apomictic phenotype has been expressed multiple times from different sexual genetic backgrounds.
Ethanolamide Oxylipins of Linolenic Acid Can Negatively Regulate Arabidopsis Seedling DevelopmentIn this work, endogenous NAE 18:3-oxylipins in various lines of Arabidopsis seedlings were detected and quantified. The results reveal a profound influence of NAE metabolism on seedling development, providing evidence that endogenous ethanolamide oxylipins may have potent biological activities during seedling establishment.
The Arabidopsis Eukaryotic Translation Initiation Factor eIF5A-2 Regulates Root Protoxylem Development by Modulating Cytokinin SignalingThis work shows that the Arabidopsis eukaryotic translation initiation factor 5A-2 genetically and physically interacts with key signaling components of the cytokinin pathway to specifically regulate root protoxylem development.
Regulation of Auxin Homeostasis and Gradients in Arabidopsis Roots through the Formation of the Indole-3-Acetic Acid Catabolite 2-Oxindole-3-Acetic AcidThis work shows that one of the major auxin degradation products in Arabidopsis roots is 2-oxindole-3-acetic acid (oxIAA). OxIAA levels increased rapidly in line with endogenous indole-3-acetic acid (IAA) levels, and oxIAA had much lower biological activity than IAA. Data presented indicate that IAA catabolism plays an important role in the regulation of auxin homeostasis and auxin gradient formation in the primary root apex.
ABI1 and PP2CA Phosphatases Are Negative Regulators of Snf1-Related Protein Kinase1 Signaling in ArabidopsisSnRK1 protein kinases are negatively regulated by the same PP2C phosphatases that repress the action of the central phytohormone abscisic acid (ABA). During environmental stress, ABA releases PP2C repression, thereby activating two key and complementary pathways and providing better protection against stress through the joined modulation of metabolism and gene expression.
Replication Protein A2c Coupled with Replication Protein A1c Regulates Crossover Formation during Meiosis in RiceThis study analyzed the role of the Replication protein A (RPA) complex in meiotic crossover formation in rice. RPA ensures that every chromosome pair possesses at least one crossover, and if this complex is mutated, chromosomes mis-segregate and plants are sterile.
Centromere Pairing in Early Meiotic Prophase Requires Active Centromeres and Precedes Installation of the Synaptonemal Complex in MaizeThis work provides evidence that centromere pairing occurs prior to telomere bouquet formation in early meiotic prophase in maize and is dependent upon centromere activity. Centromere association, in contrast with that in yeast and Drosophila, precedes ZYP1 installation. SMC6 is required for centromere pairing.
Mediation of Clathrin-Dependent Trafficking during Cytokinesis and Cell Expansion by Arabidopsis STOMATAL CYTOKINESIS DEFECTIVE ProteinsClathrin-mediated membrane trafficking is essential for cytokinesis and cell expansion. This study shows that SCD2 and SCD1, a putative Rab GEF, which coordinate to regulate cytokinesis and cell expansion in Arabidopsis, are associated with clathrin-coated vesicles and are necessary for plasma membrane endocytosis.
The PHOTOSYNTHESIS AFFECTED MUTANT68–LIKE Protein Evolved from a PSII Assembly Factor to Mediate Assembly of the Chloroplast NAD(P)H Dehydrogenase Complex in ArabidopsisAssembly factors are auxiliary proteins that promote the biogenesis of multiprotein complexes without being subunits of those. PHOTOSYNTHESIS-AFFECTED MUTANT68-LIKE (PAM68L) operates as an assembly factor of the NAD(P)H dehydrogenase complex in chloroplasts of flowering plants and derives evolutionarily from PAM68, an assembly factor of photosystem II in cyanobacteria, mosses, and plants.
Cell Growth Defect Factor1/CHAPERONE-LIKE PROTEIN OF POR1 Plays a Role in Stabilization of Light-Dependent Protochlorophyllide Oxidoreductase in Nicotiana benthamiana and ArabidopsisProtochlorophyllide oxidoreductase (POR), which catalyzes the protochlorophyllide reduction step in the chlorophyll biosynthetic pathway, is activated by light, and its substrate and product are photosensitizers. This work reports that CHAPERONE-LIKE PROTEIN OF POR1 interacts with POR isoforms in chloroplast membranes and protects POR proteins from photooxidative damage with its chaperone activity.
Convergent Evolution of Polysaccharide Debranching Defines a Common Mechanism for Starch Accumulation in Cyanobacteria and PlantsIn photosynthetic eukaryotes, starch aggregates into insoluble, semicrystalline granules through the action of a debranching enzyme of chlamydial pathogen origin. It is shown that an enzyme of analogous nature to this enzyme but of a different bacterial origin was recruited, by convergent evolution, for the same purpose in single-cell cyanobacteria.
LACCASE Is Necessary and Nonredundant with PEROXIDASE for Lignin Polymerization during Vascular Development in ArabidopsisLaccases and peroxidases are encoded by large gene families in plants, and both enzymes have been implicated in the polymerization of monolignols during lignification. Loss of function of three LACCASE genes in Arabidopsis essentially eliminates lignification in root and stem tissue, in the absence of reductions in peroxidase transcripts, indicating that laccase is essential for lignification.
Neighboring Parenchyma Cells Contribute to Arabidopsis Xylem Lignification, while Lignification of Interfascicular Fibers Is Cell AutonomousLignification provides strength to cells with secondary cell walls, such as fibers and water-conducting tracheary elements. In this study, the timing of lignification was examined using autoradiography, and targeted knockdown of lignin biosynthesis indicated that fibers undergo cell autonomous lignifications, while neighboring nonlignified cells can contribute to xylem cell lignification.
An ATP Binding Cassette Transporter Is Required for Cuticular Wax Deposition and Desiccation Tolerance in the Moss Physcomitrella patensThis study reveals that the moss Physcomitrella patens has a cuticle that is compositionally and structurally similar to those of later diverging land plants. A genetic knockout of a moss putative ABCG transporter, ABCG7, is deficient in cuticular wax accumulation and susceptible to desiccation stress. The cuticle appears to be a highly conserved evolutionary adaptation to life on land.
The Evolutionarily Conserved Iron-Sulfur Protein INDH Is Required for Complex I Assembly and Mitochondrial Translation in ArabidopsisRespiratory complex I is composed of 48 protein subunits of both nuclear and mitochondrial genetic origin. This study provides a functional characterization of INDH, which is required for the assembly of complex I but is not part of it. Unlike other complex I mutants, INDH is also involved in male and female gametogenesis and plays a role in mitochondrial translation.
In Vivo Intracellular pH Measurements in Tobacco and Arabidopsis Reveal an Unexpected pH Gradient in the Endomembrane SystemThis work combines biochemistry and live-cell imaging to perform in vivo pH measurements of different compartments of the endomembrane system in plant cells. It reports that the prevacuolar compartments are more alkaline than the trans-Golgi network and provides evidence that endosomal proton pumps and proton efflux transporters contribute to pH homeostasis.
Identification of Downstream Components of Ubiquitin-Conjugating Enzyme PHOSPHATE2 by Quantitative Membrane Proteomics in Arabidopsis RootsThis work reports quantitative membrane proteomic analysis and provides insights into the mechanism of PHO2-mediated Pi acquisition via posttranslational regulation of PHT1s. The results highlight the fundamental role of PHO2 in orchestrating Pi acquisition at the root surface and Pi loading at the xylem of root stele to maintain Pi homeostasis.
NITROGEN LIMITATION ADAPTATION, a Target of MicroRNA827, Mediates Degradation of Plasma Membrane–Localized Phosphate Transporters to Maintain Phosphate Homeostasis in ArabidopsisThis work reports that NLA mediates endocytosis and degradation of PHT1s via ubiquitination and functions cooperatively with PHO2 to regulate the abundance of PHT1s in different subcellular compartments. This finding uncovers a mechanism of modulation of Pi transport activity through the integration of miRNA-mediated posttranscriptional and ubiquitin-mediated posttranslational pathways.
Essential Role of the E3 Ubiquitin Ligase NOPPERABO1 in Schizogenous Intercellular Space Formation in the Liverwort Marchantia polymorphaNOPPERABO1 encodes a PUB-ARM–type E3 ubiquitin ligase localized at the plasma membrane that functions as a positive factor for schizogenous intercellular space formation in the liverwort Marchantia polymorpha. A significant T-DNA–tagged mutant in the emerging model liverwort, which occupies a critical position in the evolution of land plants, is reported.
Disrupting Autophagy Restores Peroxisome Function to an Arabidopsis lon2 Mutant and Reveals a Role for the LON2 Protease in Peroxisomal Matrix Protein DegradationThis study describes a screen for suppressors of peroxisomal defects that result from a dysfunctional peroxisomal protease in Arabidopsis and reveals that plant peroxisomes can be targeted by autophagy (pexophagy).
Plant Purine Nucleoside Catabolism Employs a Guanosine Deaminase Required for the Generation of Xanthosine in ArabidopsisThis work identifies a new enzyme, guanosine deaminase, which is specific for nucleoside catabolism of plants and not found in other organisms, outlining a plant-specific metabolic route. Guanosine deaminase exclusively generates xanthosine in the model plant Arabidopsis. In coffee, xanthosine is the precursor for caffeine production, which possibly requires guanosine deaminase as well.
Morphine Biosynthesis in Opium Poppy Involves Two Cell Types: Sieve Elements and LaticifersMorphine biosynthesis is shown to involve two specialized cell types in opium poppy. Most of the pathway occurs in sieve elements of the phloem, but the final three enzymes are predominant in adjacent laticifers, which are the site of morphine accumulation. The cellular localization of morphine metabolism will assist with the breeding and metabolic engineering of this important medicinal plant.
A 7-Deoxyloganetic Acid Glucosyltransferase Contributes a Key Step in Secologanin Biosynthesis in Madagascar PeriwinkleThe biosynthesis of secologanin in Madagascar periwinkle involves iridoid assembly in specialized internal phloem-associated parenchyma (IPAP) and final elaboration in leaf epidermal cells. We report the molecular cloning, functional characterization, and IPAP-associated localization of 7-deoxyloganetic acid glucosyltransferase.
The R2R3-MYB Transcription Factors MYB14 and MYB15 Regulate Stilbene Biosynthesis in Vitis viniferaThis study reports the identification and functional characterization of two stress-inducible R2R3-MYB–type transcription factors, termed MYB14 and MYB15, which regulate the stilbene biosynthetic pathway in grapevine.
p-Hydroxybenzoyl-Glucose Is a Zwitter Donor for the Biosynthesis of 7-Polyacylated Anthocyanin in DelphiniumPolyacylation of anthocyanin at the 7-position is crucial for the blue pigmentation of delphinium flowers. 7-Polyacylated anthocyanin is synthesized via a step-by-step reaction mediated by vacuolar type acyltransferases and glucosyltransferases in delphiniums. In this reaction sequence, p-hydroxybenzoyl-Glc plays a crucial role as a bifunctional donor for glucosylation and acylation.
A Rice cis-Natural Antisense RNA Acts as a Translational Enhancer for Its Cognate mRNA and Contributes to Phosphate Homeostasis and Plant Fitnesscis-natural antisense transcripts (cis-NAT) are widespread in plants and typically associated with transcriptional downregulation of their cognate sense gene. This works shows that a noncoding cis-NAT associated with the rice phosphate exporter gene PHO1;2 enhances translation of the sense PHO1;2 mRNA. Reduction of cis-NATPHO1;2 expression negatively impacts phosphate homeostasis and seed yield.
Arabidopsis J-Protein J20 Delivers the First Enzyme of the Plastidial Isoprenoid Pathway to Protein Quality ControlProtein quality control mechanisms rely on chaperones and proteases to maintain cell proteins in working conditions. This study reports the identification of a J-protein cochaperone that binds to inactive forms of a plastidial enzyme required for plant photosynthesis and development, targeting them for either proper folding or degradation in the chloroplast.
The Importance of Cardiolipin Synthase for Mitochondrial Ultrastructure, Respiratory Function, Plant Development, and Stress Responses in ArabidopsisCARDIOLIPIN SYNTHASE (CLS) catalyzes the synthesis of cardiolipin, the signature phospholipid of the mitochondrial inner membrane. Through characterization of a cls mutant in Arabidopsis, this study shows that CLS is crucial for correct mitochondrial function and development in Arabidopsis under both optimal and stress conditions.
A Mediator of Singlet Oxygen Responses in Chlamydomonas reinhardtii and Arabidopsis Identified by a Luciferase-Based Genetic Screen in Algal CellsThis work presents a genetic screen for early components of singlet oxygen signaling using the unicellular green alga Chlamydomonas and reports the identification of a small zinc finger protein, MBS, that accumulates in distinct cytosolic granules and is required for induction of singlet oxygen–dependent gene expression in Chlamydomonas and Arabidopsis.
Arabidopsis RECEPTOR-LIKE PROTEIN30 and Receptor-Like Kinase SUPPRESSOR OF BIR1-1/EVERSHED Mediate Innate Immunity to Necrotrophic FungiThis work identifies a Sclerotinia sclerotiorum elicitor that is sensed by RECEPTOR-LIKE PROTEIN30 and evokes MAMP-triggered immunity via the BRASSINOSTEROID INSENSITIVE1-ASSOCIATED RECEPTOR KINASE1 and SUPPRESSOR OF BIR1-1/EVERSHED signaling pathway. Thus, this work demonstrates the relevance of pattern recognition receptor–triggered immunity in resistance to necrotrophic fungi.
A Comprehensive Mutational Analysis of the Arabidopsis Resistance Protein RPW8.2 Reveals Key Amino Acids for Defense Activation and Protein TargetingMutational analyses of host-pathogen interface-localized Arabidopsis resistance protein RPW8.2 reveal three amino acids to be important in regulating defense function of RPW8.2 and two basic residue-enriched motifs to be critical for targeting RPW8.2 to the extrahaustorial membrane induced in epidermal cells by the powdery mildew fungus.
Crosstalk between the Unfolded Protein Response and Pathways That Regulate Pathogenic Development in Ustilago maydisBiotrophic development of fungal plant pathogens requires an intricate control mechanism that triggers morphogenetic transitions and proliferation in planta. In the corn smut fungus, the interactions between key regulators of the unfolded protein response and of the transcriptional network that regulates the pathogenic program define a developmental checkpoint critical for plant infection.
