The TOR-EIN2 axis mediates nuclear signalling to modulate plant growth.

The evolutionarily conserved target of rapamycin (TOR) kinase acts as a master regulator that coordinates cell proliferation and growth by integrating nutrient, energy, hormone and stress signals in all eukaryotes1,2. Research has focused mainly on TOR-regulated translation, but how TOR orchestrates the global transcriptional network remains unclear. Here we identify ethylene-insensitive protein 2 (EIN2), a central integrator3-5 that shuttles between the cytoplasm and the nucleus, as a direct substrate of TOR in Arabidopsis thaliana. Glucose-activated TOR kinase directly phosphorylates EIN2 to prevent its nuclear localization. Notably, the rapid global transcriptional reprogramming that is directed by glucose-TOR signalling is largely compromised in the ein2-5 mutant, and EIN2 negatively regulates the expression of a wide range of target genes of glucose-activated TOR that are involved in DNA replication, cell wall and lipid synthesis and various secondary metabolic pathways. Chemical, cellular and genetic analyses reveal that cell elongation and proliferation processes that are controlled by the glucose-TOR-EIN2 axis are decoupled from canonical ethylene-CTR1-EIN2 signalling, and mediated by different phosphorylation sites. Our findings reveal a molecular mechanism by which a central signalling hub is shared but differentially modulated by diverse signalling pathways using distinct phosphorylation codes that can be specified by upstream protein kinases.

TMK1-mediated auxin signalling regulates differential growth of the apical hook.

The plant hormone auxin has crucial roles in almost all aspects of plant growth and development. Concentrations of auxin vary across different tissues, mediating distinct developmental outcomes and contributing to the functional diversity of auxin. However, the mechanisms that underlie these activities are poorly understood. Here we identify an auxin signalling mechanism, which acts in parallel to the canonical auxin pathway based on the transport inhibitor response1 (TIR1) and other auxin receptor F-box (AFB) family proteins (TIR1/AFB receptors)1,2, that translates levels of cellular auxin to mediate differential growth during apical-hook development. This signalling mechanism operates at the concave side of the apical hook, and involves auxin-mediated C-terminal cleavage of transmembrane kinase 1 (TMK1). The cytosolic and nucleus-translocated C terminus of TMK1 specifically interacts with and phosphorylates two non-canonical transcriptional repressors of the auxin or indole-3-acetic acid (Aux/IAA) family (IAA32 and IAA34), thereby regulating ARF transcription factors. In contrast to the degradation of Aux/IAA transcriptional repressors in the canonical pathway, the newly identified mechanism stabilizes the non-canonical IAA32 and IAA34 transcriptional repressors to regulate gene expression and ultimately inhibit growth. The auxin-TMK1 signalling pathway originates at the cell surface, is triggered by high levels of auxin and shares a partially overlapping set of transcription factors with the TIR1/AFB signalling pathway. This allows distinct interpretations of different concentrations of cellular auxin, and thus enables this versatile signalling molecule to mediate complex developmental outcomes.

ROP signaling regulates spatial pattern of cell division and specification of meristem notch.

The formation of cell polarity is essential for many developmental processes such as polar cell growth and spatial patterning of cell division. A plant-specific ROP (Rho-like GTPases from Plants) subfamily of conserved Rho GTPase plays a crucial role in the regulation of cell polarity. However, the functional study of ROPs in angiosperm is challenging because of their functional redundancy. The Marchantia polymorpha genome encodes a single ROP gene, MpROP, providing an excellent genetic system to study ROP-dependent signaling pathways. Mprop knockout mutants exhibited rhizoid growth defects, and MpROP was localized at the tip of elongating rhizoids, establishing a role for MpROP in the control of polar cell growth and its functional conservation in plants. Furthermore, the Mprop knockout mutant showed defects in the formation of meristem notches associated with disorganized cell division patterns. These results reveal a critical function of MpROP in the regulation of plant development. Interestingly, these phenotypes were complemented not only by MpROP but also Arabidopsis AtROP2, supporting the conservation of ROP's function among land plants. Our results demonstrate a great potential for M. polymorpha as a powerful genetic system for functional and mechanistic elucidation of ROP signaling pathways during plant development.

Establishment of a novel minigenome system for the identification of drugs targeting Nipah virus replication.

Nipah virus (NiV) is a deadly zoonotic pathogen with high potential to cause another pandemic. Owing to biosafety concerns, studies on living NiV must be performed in biosafety level 4 (BSL-4) laboratories, which greatly hinders the development of anti-NiV drugs. To overcome this issue, minigenome systems have been developed to study viral replication and screen for antiviral drugs. This study aimed to develop two minigenome systems (transient and stable expression) based on a helper cell line expressing the NiV P, N and L proteins required to initiate NiV RNA replication. Stable minigenome cells were resistant to ribavirin, remdesivir and favipiravir but sensitive to interferons. Cells of the transient replication system were sensitive to ribavirin and favipiravir and suitable for drug screening. Our study demonstrates a feasible and effective platform for studying NiV replication and shows great potential for high-throughput drug screening in a BSL-2 laboratory environment.

Satellite-Based Global Sea Surface Oxygen Mapping and Interpretation with Spatiotemporal Machine Learning.

The assessment of dissolved oxygen (DO) concentration at the sea surface is essential for comprehending the global ocean oxygen cycle and associated environmental and biochemical processes as it serves as the primary site for photosynthesis and sea-air exchange. However, limited comprehensive measurements and imprecise numerical simulations have impeded the study of global sea surface DO and its relationship with environmental challenges. This paper presents a novel spatiotemporal information embedding machine-learning framework that provides explanatory insights into the underlying driving mechanisms. By integrating extensive in situ data and high-resolution satellite data, the proposed framework successfully generated high-resolution (0.25° × 0.25°) estimates of DO concentration with exceptional accuracy (R2 = 0.95, RMSE = 11.95 µmol/kg, and test number = 2805) for near-global sea surface areas from 2010 to 2018, uncertainty estimated to be ±13.02 µmol/kg. The resulting sea surface DO data set exhibits precise spatial distribution and reveals compelling correlations with prominent marine phenomena and environmental stressors. Leveraging its interpretability, our model further revealed the key influence of marine factors on surface DO and their implications for environmental issues. The presented machine-learning framework offers an improved DO data set with higher resolution, facilitating the exploration of oceanic DO variability, deoxygenation phenomena, and their potential consequences for environments.

miR-584-5p / Ykt6 - mediated autophagy - lysosome - exosome pathway as a critical route affecting the toxic effects of lead on HK-2 cells.

Lead is a widespread environmental pollutant with serious adverse effects on human health, but the mechanism underlying its toxicity remains elusive. This study aimed to investigate the role of miR-584-5p / Ykt6 axis in the toxic effect of lead on HK-2 cells and the related mechanism. Our data suggested that lead exposure caused significant cytotoxicity, DNA and chromosome damage to HK-2 cells. Mechanistically, lead exposure down-regulated miR-584-5p and up-regulated Ykt6 expression, consequently, autophagosomal number and autophagic flux increased, lysosomal number and activity decreased, exosomal secretion increased. Interestingly, when miR-584-5p level was enhanced with mimic, autophagosomal number and autophagic flux decreased, lysosomal number and activity increased, ultimately, exosomal secretion was down-regulated, which resulted in significant aggravated toxic effects of lead. Further, directly blocking exosomal secretion with inhibitor GW4869 also resulted in exacerbated toxic effects of lead. Herein, we conclude that miR-584-5p / Ykt6 - mediated autophagy - lysosome - exosome pathway may be a critical route affecting the toxic effects of lead on HK-2 cells. We provide a novel insight into the mechanism underlying the toxicity of lead on human cells.

Gene regulatory network controlling carpel number variation in cucumber.

The WUSCHEL-CLAVATA3 pathway genes play an essential role in shoot apical meristem maintenance and floral organ development, and under intense selection during crop domestication. The carpel number is an important fruit trait that affects fruit shape, size and internal quality in cucumber, but the molecular mechanism remains elusive. Here, we found that CsCLV3 expression was negatively correlated with carpel number in cucumber cultivars. CsCLV3-RNAi led to increased number of petals and carpels, whereas overexpression of CsWUS resulted in more sepals, petals and carpels, suggesting that CsCLV3 and CsWUS function as a negative and a positive regulator for carpel number variation, respectively. Biochemical analyses indicated that CsWUS directly bound to the promoter of CsCLV3 and activated its expression. Overexpression of CsFUL1A , a FRUITFULL-like MADS-box gene, resulted in more petals and carpels. CsFUL1A can directly bind to the CsWUS promoter to stimulate its expression. Furthermore, we found that auxin participated in carpel number variation in cucumber through interaction of CsARF14 with CsWUS. Therefore, we have identified a gene regulatory pathway involving CsCLV3, CsWUS, CsFUL1A and CsARF14 in determining carpel number variation in an important vegetable crop - cucumber.

FATTY ACID DESATURASE5 Is Required to Induce Autoimmune Responses in Gigantic Chloroplast Mutants of Arabidopsis.

Chloroplasts mediate genetically controlled cell death via chloroplast-to-nucleus retrograde signaling. To decipher the mechanism, we examined chloroplast-linked lesion-mimic mutants of Arabidopsis (Arabidopsis thaliana) deficient in plastid division, thereby developing gigantic chloroplasts (GCs). These GC mutants, including crumpled leaf (crl), constitutively express immune-related genes and show light-dependent localized cell death (LCD), mirroring typical autoimmune responses. Our reverse genetic approach excludes any potential role of immune/stress hormones in triggering LCD. Instead, transcriptome and in silico analyses suggest that reactive electrophile species (RES) generated via oxidation of polyunsaturated fatty acids (PUFAs) or lipid peroxidation-driven signaling may induce LCD. Consistent with these results, the one of the suppressors of crl, dubbed spcrl4, contains a causative mutation in the nuclear gene encoding chloroplast-localized FATTY ACID DESATURASE5 (FAD5) that catalyzes the conversion of palmitic acid (16:0) to palmitoleic acid (16:1). The loss of FAD5 in the crl mutant might attenuate the levels of RES and/or lipid peroxidation due to the reduced levels of palmitic acid-driven PUFAs, which are prime targets of reactive oxygen species. The fact that fad5 also compromises the expression of immune-related genes and the development of LCD in other GC mutants substantiates the presence of an intrinsic retrograde signaling pathway, priming the autoimmune responses in a FAD5-dependent manner.

CsIVP functions in vasculature development and downy mildew resistance in cucumber.

Domesticated crops with high yield and quality are frequently susceptible to pathogen attack, whereas enhancement of disease resistance generally compromises crop yield. The underlying mechanisms of how plant development and disease resistance are coordinately programed remain elusive. Here, we showed that the basic Helix-Loop-Helix (bHLH) transcription factor Cucumis sativus Irregular Vasculature Patterning (CsIVP) was highly expressed in cucumber vascular tissues. Knockdown of CsIVP caused severe vasculature disorganization and abnormal organ morphogenesis. CsIVP directly binds to vascular-related regulators YABBY5 (CsYAB5), BREVIPEDICELLUS (CsBP), and AUXIN/INDOLEACETIC ACIDS4 (CsAUX4) and promotes their expression. Knockdown of CsYAB5 resulted in similar phenotypes as CsIVP-RNA interference (RNAi) plants, including disturbed vascular configuration and abnormal organ morphology. Meanwhile, CsIVP-RNAi plants were more resistant to downy mildew and accumulated more salicylic acid (SA). CsIVP physically interacts with NIM1-INTERACTING1 (CsNIMIN1), a negative regulator in the SA signaling pathway. Thus, CsIVP is a novel vasculature regulator functioning in CsYAB5-mediated organ morphogenesis and SA-mediated downy mildew resistance in cucumber.

Full genome sequence of a novel iflavirus from the aster leafhopper Macrosteles fascifrons.

The aster leafhopper Macrosteles fascifrons is a common insect pest that feeds on rice and other plants and may serve as a vector to transmit various viruses. Here, we discovered a novel virus from M. fascifrons using metagenomic sequencing. We obtained its complete genome sequence by contig assembly and rapid amplification of cDNA ends, and verified the genome sequence by Sanger sequencing of overlapping segments. Based on homology search and phylogenetic analysis, the new virus belongs to the family Iflaviridae and it is tentatively named "Macrosteles fascifrons iflavirus 1" (MfIV1). Excluding the poly(A) tail, the MfIV1 genome is 10,581 nucleotides in length and it is predicted to encode a polyprotein of 3119 amino acids long, which is likely further processed to several polypeptides with conserved domains, including two rhinovirus like (rhv-like) capsid domains, a cricket paralysis virus (CRPV) capsid domain, a helicase domain, and an RNA-dependent RNA polymerase (RdRp) domain. BLAST searches show that the highest amino acid sequence identity between the capsid proteins of MfIV1 and those of other reported iflaviruses is 60.22%, indicating that MfIV1 is a new member in the family Iflaviridae.

Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels.

Transposable elements (TEs) make up a large portion of plant genomes and play a vital role in genome structure, function, and evolution. Cultivated strawberry (Fragaria x ananassa) is one of the most important fruit crops, and its octoploid genome was formed through several rounds of genome duplications from diploid ancestors. Here, we built a pan-genome TE library for the Fragaria genus using ten published strawberry genomes at different ploidy levels, including seven diploids, one tetraploid, and two octoploids, and performed comparative analysis of TE content in these genomes. The TEs comprise 51.83% (F. viridis) to 60.07% (F. nilgerrensis) of the genomes. Long terminal repeat retrotransposons (LTR-RTs) are the predominant TE type in the Fragaria genomes (20.16% to 34.94%), particularly in F. iinumae (34.94%). Estimating TE content and LTR-RT insertion times revealed that species-specific TEs have shaped each strawberry genome. Additionally, the copy number of different LTR-RT families inserted in the last one million years reflects the genetic distance between Fragaria species. Comparing cultivated strawberry subgenomes to extant diploid ancestors showed that F. vesca and F. iinumae are likely the diploid ancestors of the cultivated strawberry, but not F. viridis. These findings provide new insights into the TE variations in the strawberry genomes and their roles in strawberry genome evolution.

Uncoupled Expression of Nuclear and Plastid Photosynthesis-Associated Genes Contributes to Cell Death in a Lesion Mimic Mutant.

Chloroplast-to-nucleus retrograde signaling is essential for the coupled expression of photosynthesis-associated nuclear genes (PhANGs) and plastid genes (PhAPGs) to ensure the functional status of chloroplasts (Cp) in plants. Although various signaling components involved in the process have been identified in Arabidopsis (Arabidopsis thaliana), the biological relevance of such coordination remains an enigma. Here, we show that the uncoupled expression of PhANGs and PhAPGs contributes to the cell death in the lesion simulating disease1 (lsd1) mutant of Arabidopsis. A daylength-dependent increase of salicylic acid (SA) appears to rapidly up-regulate a gene encoding SIGMA FACTOR BINDING PROTEIN1 (SIB1), a transcriptional coregulator, in lsd1 before the onset of cell death. The dual targeting of SIB1 to the nucleus and the Cps leads to a simultaneous up-regulation of PhANGs and down-regulation of PhAPGs. Consequently, this disrupts the stoichiometry of photosynthetic proteins, especially in PSII, resulting in the generation of the highly reactive species singlet oxygen (1O2) in Cps. Accordingly, inactivation of the nuclear-encoded Cp protein EXECUTER1, a putative 1O2 sensor, significantly attenuates the lsd1-conferred cell death. Together, these results provide a pathway from the SA- to the 1O2-signaling pathway, which are intertwined via the uncoupled expression of PhANGs and PhAPGs, contributing to the lesion-mimicking cell death in lsd1.

A Functional Allele of CsFUL1 Regulates Fruit Length through Repressing CsSUP and Inhibiting Auxin Transport in Cucumber.

Fruit length is a prominent agricultural trait during cucumber (Cucumis sativus) domestication and diversifying selection; however, the regulatory mechanisms of fruit elongation remain elusive. We identified two alleles of the FRUITFULL (FUL)-like MADS-box gene CsFUL1 with 3393C/A Single Nucleotide Polymorphism variation among 150 cucumber lines. Whereas CsFUL1A was specifically enriched in the long-fruited East Asian type cucumbers (China and Japan), the CsFUL1C allele was randomly distributed in cucumber populations, including wild and semiwild cucumbers. CsFUL1A knockdown led to further fruit elongation in cucumber, whereas elevated expression of CsFUL1A resulted in significantly shorter fruits. No effect on fruit elongation was detected when CsFUL1C expression was modulated, suggesting that CsFUL1A is a gain-of-function allele in long-fruited cucumber that acts as a repressor during diversifying selection of East Asian cucumbers. Furthermore, CsFUL1A binds to the CArG-box in the promoter region of SUPERMAN, a regulator of cell division and expansion, to repress its expression. Additionally, CsFUL1A inhibits the expression of auxin transporters PIN-FORMED1 (PIN1) and PIN7, resulting in decreases in auxin accumulation in fruits. Together, our work identifies an agriculturally important allele and suggests a strategy for manipulating fruit length in cucumber breeding that involves modulation of CsFUL1A expression.

Predicting the molecular subtype of breast cancer and identifying interpretable imaging features using machine learning algorithms.

OBJECTIVES: To evaluate the performance of interpretable machine learning models in predicting breast cancer molecular subtypes. METHODS: We retrospectively enrolled 600 patients with invasive breast carcinoma between 2012 and 2019. The patients were randomly divided into a training (n = 450) and a testing (n = 150) set. The five constructed models were trained based on clinical characteristics and imaging features (mammography and ultrasonography). The model classification performances were evaluated using the area under the receiver operating characteristic (ROC) curve (AUC), accuracy, sensitivity, and specificity. Shapley additive explanation (SHAP) technique was used to interpret the optimal model output. Then we choose the optimal model as the assisted model to evaluate the performance of another four radiologists in predicting the molecular subtype of breast cancer with or without model assistance, according to mammography and ultrasound images. RESULTS: The decision tree (DT) model performed the best in distinguishing triple-negative breast cancer (TNBC) from other breast cancer subtypes, yielding an AUC of 0.971; accuracy, 0.947; sensitivity, 0.905; and specificity, 0.941. The accuracy, sensitivity, and specificity of all radiologists in distinguishing TNBC from other molecular subtypes and Luminal breast cancer from other molecular subtypes have significantly improved with the assistance of DT model. In the diagnosis of TNBC versus other subtypes, the average sensitivity, average specificity, and average accuracy of less experienced and more experienced radiologists increased by 0.090, 0.125, 0.114, and 0.060, 0.090, 0.083, respectively. In the diagnosis of Luminal versus other subtypes, the average sensitivity, average specificity, and average accuracy of less experienced and more experienced radiologists increased by 0.084, 0.152, 0.159, and 0.020, 0.100, 0.048. CONCLUSIONS: This study established an interpretable machine learning model to differentiate between breast cancer molecular subtypes, providing additional values for radiologists. KEY POINTS: • Interpretable machine learning model (MLM) could help clinicians and radiologists differentiate between breast cancer molecular subtypes. • The Shapley additive explanations (SHAP) technique can select important features for predicting the molecular subtypes of breast cancer from a large number of imaging signs. • Machine learning model can assist radiologists to evaluate the molecular subtype of breast cancer to some extent.

A deep learning-machine learning fusion approach for the classification of benign, malignant, and intermediate bone tumors.

OBJECTIVES: To build and validate deep learning and machine learning fusion models to classify benign, malignant, and intermediate bone tumors based on patient clinical characteristics and conventional radiographs of the lesion. METHODS: In this retrospective study, data were collected with pathologically confirmed diagnoses of bone tumors between 2012 and 2019. Deep learning and machine learning fusion models were built to classify tumors as benign, malignant, or intermediate using conventional radiographs of the lesion and potentially relevant clinical data. Five radiologists compared diagnostic performance with and without the model. Diagnostic performance was evaluated using the area under the curve (AUC). RESULTS: A total of 643 patients' (median age, 21 years; interquartile range, 12-38 years; 244 women) 982 radiographs were included. In the test set, the binary category classification task, the radiological model of classification for benign/not benign, malignant/nonmalignant, and intermediate/not intermediate had AUCs of 0.846, 0.827, and 0.820, respectively; the fusion models had an AUC of 0.898, 0.894, and 0.865, respectively. In the three-category classification task, the radiological model achieved a macro average AUC of 0.813, and the fusion model had a macro average AUC of 0.872. In the observation test, the mean macro average AUC of all radiologists was 0.819. With the three-category classification fusion model support, the macro AUC improved by 0.026. CONCLUSION: We built, validated, and tested deep learning and machine learning models that classified bone tumors at a level comparable with that of senior radiologists. Model assistance may somewhat help radiologists' differential diagnoses of bone tumors. KEY POINTS: • The deep learning model can be used to classify benign, malignant, and intermediate bone tumors. • The machine learning model fusing information from radiographs and clinical characteristics can improve the classification capacity for bone tumors. • The diagnostic performance of the fusion model is comparable with that of senior radiologists and is potentially useful as a complement to radiologists in a bone tumor differential diagnosis.

Full genome sequence of a novel iflavirus from the leafhopper Recilia dorsalis.

The leafhopper Recilia dorsalis (family Cicadellidae, tribe Deltocephalini) is a common pest of rice and a transmitter of various viruses. Here, we discovered a novel virus in an R. dorsalis sample and determined its complete genome sequence by metagenomic sequencing and rapid amplification of cDNA ends. Based on a homology search and phylogenetic analysis, we show that the new virus belongs to the genus Iflavirus, family Iflaviridae, and we have tentatively named it "Recilia dorsalis iflavirus 1" (RdIV1). Excluding the polyA tail, the RdIV1 genome is 10,986 nucleotides in length and is predicted to encode a 3,195-amino-acid-long polyprotein that possesses the typical domains of iflaviruses: two rhinovirus-like (rhv-like) capsid domains, a cricket paralysis virus-like (CRPV-like) capsid domain, a helicase domain, a protease domain, and an RNA-dependent RNA polymerase (RdRp) domain. BLAST searches showed that the RdIV1 genome has the highest amino sequence identity (73.8%) in the coat protein region to Euscelidius variegatus virus 1 (EVV-1), a member of to the genus Iflavirus, indicating that RdIV1 can be classified as a new iflavirus.

Regulation of active DNA demethylation by an α-crystallin domain protein in Arabidopsis.

DNA methylation patterns are dynamically controlled by DNA methylation and active DNA demethylation, but the mechanisms of regulation of active DNA demethylation are not well understood. Through forward genetic screens for Arabidopsis mutants showing DNA hypermethylation at specific loci and increased silencing of reporter genes, we identified IDM2 (increased DNA methylation 2) as a regulator of DNA demethylation and gene silencing. IDM2 dysfunction causes DNA hypermethylation and silencing of reporter genes and some endogenous genes. These effects of idm2 mutations are similar to those of mutations in IDM1, a regulator of active DNA demethylation. IDM2 encodes an α-crystallin domain protein in the nucleus. IDM2 and IDM1 interact physically and partially colocalize at discrete subnuclear foci. IDM2 is required for the full activity of H3K18 acetylation but not H3K23 acetylation of IDM1 in planta. Our results suggest that IDM2 functions in active DNA demethylation and in antisilencing by regulating IDM1.

The Rho-family GTPase OsRac1 controls rice grain size and yield by regulating cell division.

Grain size is a key factor for determining grain yield in crops and is a target trait for both domestication and breeding, yet the mechanisms underlying the regulation of grain size are largely unclear. Here we show that the grain size and yield of rice (Oryza sativa) is positively regulated by ROP GTPase (Rho-like GTPase from plants), a versatile molecular switch modulating plant growth, development, and responses to the environment. Overexpression of rice OsRac1ROP not only increases cell numbers, resulting in a larger spikelet hull, but also accelerates grain filling rate, causing greater grain width and weight. As a result, OsRac1 overexpression improves grain yield in O. sativa by nearly 16%. In contrast, down-regulation or deletion of OsRac1 causes the opposite effects. RNA-seq and cell cycle analyses suggest that OsRac1 promotes cell division. Interestingly, OsRac1 interacts with and regulates the phosphorylation level of OsMAPK6, which is known to regulate cell division and grain size in rice. Thus, our findings suggest OsRac1 modulates rice grain size and yield by influencing cell division. This study provides insights into the molecular mechanisms underlying the control of rice grain size and suggests that OsRac1 could serve as a potential target gene for breeding high-yield crops.

CsBRC1 inhibits axillary bud outgrowth by directly repressing the auxin efflux carrier CsPIN3 in cucumber.

Shoot branching is an important agronomic trait that directly determines plant architecture and affects crop productivity. To promote crop yield and quality, axillary branches need to be manually removed during cucumber production for fresh market and thus are undesirable. Auxin is well known as the primary signal imposing for apical dominance and acts as a repressor for lateral bud outgrowth indirectly. The TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) family gene BRANCHED1 (BRC1) has been shown to be the central integrator for multiple environmental and developmental factors that functions locally to inhibit shoot branching. However, the direct molecular link between auxin and BRC1 remains elusive. Here we find that cucumber BRANCHED1 (CsBRC1) is expressed in axillary buds and displays a higher expression level in cultivated cucumber than in its wild ancestor. Knockdown of CsBRC1 by RNAi leads to increased bud outgrowth and reduced auxin accumulation in buds. We further show that CsBRC1 directly binds to the auxin efflux carrier PIN-FORMED (CsPIN3) and negatively regulates its expression in vitro and in vivo. Elevated expression of CsPIN3 driven by the CsBRC1 promoter results in highly branched cucumber with decreased auxin levels in lateral buds. Therefore, our data suggest that CsBRC1 inhibits lateral bud outgrowth by direct suppression of CsPIN3 functioning and thus auxin accumulation in axillary buds in cucumber, providing a strategy to breed for cultivars with varying degrees of shoot branching grown in different cucumber production systems.

HISTONE DEACETYLASE 9 Functions with Polycomb Silencing to Repress FLOWERING LOCUS C Expression.

Polycomb repressive complex 2 (PRC2) catalyzes repressive histone 3 Lys-27 trimethylation (H3K27me3) to mediate genome-wide transcriptional repression in plants and animals. PRC2 controls various developmental processes in plants and plays a critical role in the developmental transition to flowering. FLOWERING LOCUS C (FLC), first identified in Arabidopsis (Arabidopsis thaliana), is a potent floral repressor in crucifers and some other plants that is subjected to complex regulation. Here, we show that HISTONE DEACETYLASE 9 (HDA9)-mediated H3K27 deacetylation is required for PRC2-mediated H3K27me3 in Arabidopsis. We further demonstrate that through physical association with the epigenome readers VP1/ABI3-LIKE 1 (VAL1) and VAL2, which recognize a cis-regulatory element at the FLC locus, HDA9 and PRC2 function in concert to mediate H3K27 deacetylation and subsequent trimethylation at this residue. This leads to FLC repression in the rapid-cycling Arabidopsis accessions. Our study uncovers roles for HDA9 in PRC2-mediated H3K27me3, FLC repression, and flowering-time regulation.