Table of Contents
IN BRIEF
LARGE-SCALE BIOLOGY ARTICLE
Machine Learning–Based Differential Network Analysis: A Study of Stress-Responsive Transcriptomes in ArabidopsisThis work presents a machine learning–based method for transcriptome analysis via comparison of gene coexpression networks, which outperforms traditional statistical tests at identifying stress-related genes. Analysis of an Arabidopsis stress expression data set led to the prediction of candidate stress-related genes showing expression and network changes in response to multiple abiotic stresses.
RESEARCH ARTICLES
The BAF60 Subunit of the SWI/SNF Chromatin-Remodeling Complex Directly Controls the Formation of a Gene Loop at FLOWERING LOCUS C in ArabidopsisIt is shown that BAF60, a subunit of the chromatin-remodeling complex SWI/SNF, induces a change in the floral repressor FLOWERING LOCUS C at the high-order chromatin level, thereby repressing the photoperiod flowering pathway in Arabidopsis. Specifically, BAF60 modulates histone density, composition, and posttranslational modification, thereby controlling gene loop formation at FLOWERING LOCUS C.
Structural Features Determining Flower-Promoting Activity of Arabidopsis FLOWERING LOCUS TFT, also known as florigen, activates flowering, while the closely related TFL1 represses flowering. By mutating most FT residues, the authors identified a comprehensive set of mutations that convert FT into a TFL1 mimic. These mutations are all predicted to change the surface charge, pointing to important differences in FT and TFL1 interactions with other proteins.
Photoperiodic Control of Carbon Distribution during the Floral Transition in ArabidopsisThe distribution of carbon resources from starch to soluble sugars is crucial to fuel the diverse physiological processes that take place during the floral transition. A multidisciplinary study supports the control of sugar mobilization in Arabidopsis during photoperiodic flowering through regulation of GRANULE BOUND STARCH SYNTHASE expression by the key photoperiodic regulator CONSTANS.
Tomato GOLDEN2-LIKE Transcription Factors Reveal Molecular Gradients That Function during Fruit Development and RipeningMany fruits develop as chloroplast-rich organs that transition to ripening, where photosynthesis wanes and flavor, aroma, and nutritional metabolites predominate. Regulatory genes are shown to influence the numbers and patterns of chloroplast distribution in fruit and leaves and that chloroplast abundance in green fruit is related to the nutrition and quality attributes of ripe fruit.
Profiling of Translatomes of in Vivo–Grown Pollen Tubes Reveals Genes with Roles in Micropylar Guidance during Pollination in ArabidopsisThis work described the use of a method for the specific isolation of ribosome-associated mRNAs of in vivo–grown pollen tubes to identify over 500 genes with transcripts highly enriched or specific to in vivo–grown pollen tubes. T-DNA insertion alleles of a number of these genes conferred defects in late stages of the pollination process by haploid gametes.
Arabidopsis DAYU/ABERRANT PEROXISOME MORPHOLOGY9 Is a Key Regulator of Peroxisome Biogenesis and Plays Critical Roles during Pollen Maturation and Germination in PlantaPeroxisomes are dynamic single-membrane organelles in eukaryotes. Peroxins are essential proteins required for peroxisome biogenesis and play multiple roles in development and growth. DAU/APEM9, a recently identified peroxin, plays a critical role in peroxisome biogenesis, morphology, and function during pollen maturation and germination in planta.
A Pollen Coat–Inducible Autoinhibited Ca2+-ATPase Expressed in Stigmatic Papilla Cells Is Required for Compatible Pollination in the BrassicaceaeIn the Brassicaceae, the pollen coat of compatible pollen grains contains signaling factors that induce Ca2+ export from the stigmatic papilla cells. This Ca2+ export is performed by at least one Ca2+ pump, ACA13, and is required for pollen germination and successful pollination.
STENOFOLIA Recruits TOPLESS to Repress ASYMMETRIC LEAVES2 at the Leaf Margin and Promote Leaf Blade Outgrowth in Medicago truncatulaThe M. truncatula WOX protein STENOFOLIA (STF) physically interacts with TOPLESS (Mt-TPL) and TPL-related corepressors via its conserved WUS box and STF box motifs and directly represses ASYMMETRIC LEAVES2 expression at the leaf margin to promote leaf blade outgrowth in M. truncatula.
The Ubiquitin Receptor DA1 Regulates Seed and Organ Size by Modulating the Stability of the Ubiquitin-Specific Protease UBP15/SOD2 in ArabidopsisThis work shows that the ubiquitin receptor DA1 genetically and physically interacts with the ubiquitin-specific protease UBP15 to regulate seed size in Arabidopsis, suggesting that DA1 and UBP15 are promising targets for crop improvement.
Lotus japonicus Cytokinin Receptors Work Partially Redundantly to Mediate Nodule FormationIn Lotus japonicus, the LHK1 cytokinin receptor performs an essential function but also works partially redundantly with LHK1A and LHK3 to mediate nodule primordium formation within the root cortex. LHK1 is also expressed in the root epidermis, where it likely participates in signaling to restrict rhizobial infection.
ABD1 Is an Arabidopsis DCAF Substrate Receptor for CUL4-DDB1–Based E3 Ligases That Acts as a Negative Regulator of Abscisic Acid SignalingCULLIN4-based E3 ubiquitin ligases and their associated substrate receptors, DDB1-CUL4–associated factors (DCAFs), regulate the selective ubiquitination of proteins, which ultimately leads to their degradation. This study reports that a DCAF, ABD1 (for ABA-hypersensitive DCAF1), directly binds to and affects the stability of ABI5, a central transcription factor in abscisic acid signaling.
Targeted Degradation of Abscisic Acid Receptors Is Mediated by the Ubiquitin Ligase Substrate Adaptor DDA1 in ArabidopsisCULLIN4-RING E3 ubiquitin ligases target proteins for proteasomal degradation, thus regulating plant developmental and stress responses. The ubiquitin ligase substrate adaptor DDA1 binds to and promotes destabilization of the abscisic acid (ABA) receptor PYL8, thereby attenuating ABA-mediated responses through desensitization, and ABA counteracts the destabilization of PYL8.
The Synaptonemal Complex Protein ZYP1 Is Required for Imposition of Meiotic Crossovers in BarleyThe number of genetic crossovers during meiosis, and the potential for creating novel variation, is influenced by the ZYP1 protein. When ZYP1 is depleted in Arabidopsis, fewer crossovers occur, whereas in rice, more crossovers have been reported. Here, we show that barley plants with very reduced amounts of ZYP1 make far fewer crossovers, although the localization of crossovers is not affected.
Analysis of Complementarity Requirements for Plant MicroRNA Targeting Using a Nicotiana benthamiana Quantitative Transient AssayThis study uses a quantitative, transient approach in Nicotiana benthamiana to measure the complementarity between plant miRNAs and their targets required to achieve measurable target repression at both the mRNA and protein levels.
Imaging of Endogenous Messenger RNA Splice Variants in Living Cells Reveals Nuclear Retention of Transcripts Inaccessible to Nonsense-Mediated Decay in ArabidopsisAlternatively spliced transcripts often have different fates depending on their cellular locations. This article presents an easily applicable method using molecular beacons and standard laser scanning microscopy to monitor endogenous transcripts within a plant cell. The results show that intron retention transcripts, which are insensitive to nonsensemediated decay, are localized to the nucleus.
Synthetic Lethality in the Tobacco Plastid Ribosome and Its Rescue at Elevated Growth TemperaturesThis work presents a systematic analysis of nonessential plastid ribosomal proteins and reports that the combined deletion of two ribosomal protein genes (rps15 and rpl33) that individually can be deleted without causing a mutant phenotype results in synthetic lethality and loss of autotrophic growth.
RAP, the Sole Octotricopeptide Repeat Protein in Arabidopsis, Is Required for Chloroplast 16S rRNA MaturationChloroplast gene expression is mainly regulated by nucleus-encoded helical repeat proteins, like PPR, TPR, and OPR proteins. This study identifies a molecular role for RAP, the only OPR protein in Arabidopsis, in chloroplast 16S rRNA maturation. Furthermore, it provides evidence that the nucleoid is the relevant suborganellar location for rRNA maturation in the chloroplast.
AUTOPHAGY-RELATED11 Plays a Critical Role in General Autophagy- and Senescence-Induced Mitophagy in ArabidopsisThe ATG1/13 kinase complex that regulates autophagy also includes ATG11 and ATG101, with ATG11 helping regulate the phosphorylation and turnover of ATG1 and ATG13, tether the complex to developing autophagic structures, and promote the delivery of autophagic vesicles to the vacuole. ATG11 and other autophagy factors also direct the elimination of mitochondria via a vacuolar mitophagic process.
SnRK1A-Interacting Negative Regulators Modulate the Nutrient Starvation Signaling Sensor SnRK1 in Source-Sink Communication in Cereal Seedlings under Abiotic StressThis work identifies a family of plant-specific SnRK1A-interacting negative regulators, SKINs, which repress SnRK1A-dependent sugar/nutrient starvation signaling by inhibiting the induction of enzyme expression facilitating nutrient mobilization under abiotic stress conditions.
The bHLH Transcription Factor HBI1 Mediates the Trade-Off between Growth and Pathogen-Associated Molecular Pattern–Triggered Immunity in ArabidopsisHBI1 is activated posttranscriptionally by growth-promoting hormonal and environmental signals through the triple-HLH/bHLH cascade but is repressed transcriptionally by pathogen-associated molecular pattern signals. HBI1 both activates growth and inhibits immunity, thereby acting as a crosstalk node that mediates the trade-off between growth and immunity.
