BBX9 forms feedback loops with PIFs and BBX21 to promote photomorphogenic development.

Light is one of the most essential environmental factors that tightly and precisely control various physiological and developmental processes in plants. B-box CONTAINING PROTEINs (BBXs) play central roles in the regulation of light-dependent development. In this study, we report that BBX9 is a positive regulator of light signaling. BBX9 interacts with the red light photoreceptor PHYTOCHROME B (phyB) and transcription factors PHYTOCHROME-INTERACTING FACTORs (PIFs). phyB promotes the stabilization of BBX9 in light, while BBX9 inhibits the transcriptional activation activity of PIFs. In turn, PIFs directly bind to the promoter of BBX9 to repress its transcription. On the other hand, BBX9 associates with the positive regulator of light signaling, BBX21, and enhances its biochemical activity. BBX21 associates with the promoter regions of BBX9 and transcriptionally up-regulates its expression. Collectively, this study unveiled that BBX9 forms a negative feedback loop with PIFs and a positive one with BBX21 to ensure that plants adapt to fluctuating light conditions.

A warm temperature-released negative feedback loop fine-tunes PIF4-mediated thermomorphogenesis in Arabidopsis.

Plants can sense temperature changes and adjust their growth accordingly. In Arabidopsis, high ambient temperatures stimulate stem elongation by activating a key thermoresponsive regulator, PHYTOCHROME INTERACTING FACTOR 4 (PIF4). Here, we show that warmth promotes the nighttime transcription of GI, which is necessary for the high temperature-induced transcription of TOC1. Genetic analyses suggest that GI prevents excessive thermoresponsive growth by inhibiting PIF4, with this regulatory mechanism being partially reliant on TOC1. GI transcription is repressed by ELF3 and HY5, which concurrently inhibit PIF4 expression and activity. Temperature elevation causes the deactivation or degradation of ELF3 and HY5, leading to PIF4 activation and relief of GI transcriptional repression at high temperatures. This allows PIF4 to further activate GI transcription in response to elevated temperatures. GI, in turn, inhibits PIF4, establishing a negative feedback loop that fine-tunes PIF4 activity. In addition, we demonstrate that ELF3, HY5, and PIF4 regulate GI transcription by modulating the enrichment of histone variant H2A.Z at the GI locus. Together, our findings suggest that thermal release of a negative feedback loop finely adjusts plant thermomorphogenesis.

The GmSTF1/2-GmBBX4 negative feedback loop acts downstream of blue-light photoreceptors to regulate isoflavonoid biosynthesis in soybean.

Isoflavonoids, secondary metabolites derived from the phenylalanine pathway, are predominantly biosynthesized in legumes, especially soybean (Glycine max). They are not only essential for plant responses to biotic and abiotic stresses but also beneficial to human health. In this study, we report that light signaling controls isoflavonoid biosynthesis in soybean. Blue-light photoreceptors (GmCRY1s, GmCRY2s, GmPHOT1s, and GmPHOT2s) and the transcription factors GmSTF1 and GmSTF2 promote isoflavonoid accumulation, whereas the E3 ubiquitin ligase GmCOP1b negatively regulates isoflavonoid biosynthesis. GmPHOT1s and GmPHOT2s stabilize GmSTF1/2, whereas GmCOP1b promotes the degradation of these two proteins in soybean. GmSTF1/2 regulate the expression of approximately 27.9% of the genes involved in soybean isoflavonoid biosynthesis, including GmPAL2.1, GmPAL2.3, and GmUGT2. They also repress the expression of GmBBX4, a negative regulator of isoflavonoid biosynthesis in soybean. In addition, GmBBX4 physically interacts with GmSTF1 and GmSTF2 to inhibit their transcriptional activation activity toward target genes related to isoflavonoid biosynthesis. Thus, GmSTF1/2 and GmBBX4 form a negative feedback loop that acts downstream of photoreceptors in the regulation of isoflavonoid biosynthesis. Our study provides novel insights into the control of isoflavonoid biosynthesis by light signaling in soybean and will contribute to the breeding of soybean cultivars with high isoflavonoid content through genetic and metabolic engineering.

Computational Determination of the Mechanism of the Palladium-Catalyzed Domino Reaction of ortho-Iodostyrene, Oxanorbornadiene, and Phenylboronic Acid.

The palladium-catalyzed three-component domino reaction of ortho-iodostyrene, 2,3-dicarbomethoxy-7-oxanorbornadiene (ONBD), and phenylboronic acid discovered by the Lautens group provides a convenient method to synthesize indenes derivatives. Herein, density functional theory (DFT) calculations were employed to explore the detailed mechanism of this domino reaction. The computational results suggest that the alkene-insertion-first and the transmetalation-first mechanisms are competitive, and the former mechanism is slightly more favorable because of the difficult intramolecular alkene insertion of the alkyl-PdII-aryl than alkyl-PdII-I complex. Further analysis on substituents of ONBD unveils the impacts of noncovalent interactions and electronic effect on the rate-determining retro-Diels-Alder process. The understanding of this domino reaction has important implications for developing a novel palladium-catalyzed domino reaction with a retro-Diels-Alder strategy.

Computational Elucidation on the Conformational Control of Selectivity in Intramolecular Ring-Closing Metathesis vs Intermolecular Homometathesis.

The ring-closing metathesis reaction of diene plays an important role in the construction of cyclic compounds. In this research, density functional theory (DFT) calculations were conducted to elucidate the mechanisms and origins of the selectivity of ring-closing metathesis and homometathesis. The computational results suggest that the selectivity is determined by the substrate conformation. For the ester-tethered substrate, the homometathesis is more favorable, due to the planar structure of ester facilitating the conjugative effect of the formed E-homometathesis product. For the amide-tethered substrate, the ring-closing metathesis product is the only observed product because the steric hindrance of N-substituents disfavors homometathesis.

Coordinated histone variant H2A.Z eviction and H3.3 deposition control plant thermomorphogenesis.

Plants can sense temperature changes and adjust their development and morphology accordingly in a process called thermomorphogenesis. This phenotypic plasticity implies complex mechanisms regulating gene expression reprogramming in response to environmental alteration. Histone variants often associate with specific chromatin states; yet, how their deposition/eviction modulates transcriptional changes induced by environmental cues remains elusive. In Arabidopsis thaliana, temperature elevation-induced transcriptional activation at thermo-responsive genes entails the chromatin eviction of a histone variant H2A.Z by INO80, which is recruited to these loci via interacting with a key thermomorphogenesis regulator PIF4. Here, we show that both INO80 and the deposition chaperones of another histone variant H3.3 associate with ELF7, a critical component of the transcription elongator PAF1 complex. H3.3 promotes thermomorphogenesis and the high temperature-enhanced RNA Pol II transcription at PIF4 targets, and it is broadly required for the H2A.Z removal-induced gene activation. Reciprocally, INO80 and ELF7 regulate H3.3 deposition, and are necessary for the high temperature-induced H3.3 enrichment at PIF4 targets. Our findings demonstrate close coordination between H2A.Z eviction and H3.3 deposition in gene activation induced by high temperature, and pinpoint the importance of histone variants dynamics in transcriptional regulation.

Z-Trisubstituted α,ß-Unsaturated Esters and Acid Fluorides through Stereocontrolled Catalytic Cross-Metathesis.

Catalytic cross-metathesis (CM) reactions that can generate trisubstituted alkenes in high stereoisomeric purity are important but remain limited in scope. Here, CM reactions are introduced that generate Z-trisubstituted α-methyl, α,ß-unsaturated, alkyl and aryl esters, thiol esters, and acid fluorides. Transformations are promoted by a Mo bis-aryloxide, a monoaryloxide pyrrolide, or a monoaryloxide chloride complex; air-stable and commercially available paraffin tablets containing a Mo complex may also be used. Alkyl, aryl, and silyl carboxylic esters as well as thiol esters and acid fluoride reagents are either purchasable or can be prepared in one step. Products were obtained in 55-95% yield and in 88:12->98:2 Z/E ratio (typically >95:5). The applicability of the approach is highlighted by a two-step conversion of citronellol to an isomintlactone precursor (1.7 g, 73% yield, and 97:3 Z/E) and a single-step transformation of lanosterol acetate to 3-epi-anwuweizic acid (72% yield and 94:6 Z/E). Included are the outcomes of DFT studies, regarding several initially puzzling catalyst activity trends, providing the following information: (1) it is key that a disubstituted Mo alkylidene, generated by a competing homo-metathesis (HM) pathway, can re-enter the productive CM cycle. (2) Whereas in a CM cycle the formation of a molybdacyclobutane is likely turnover-limiting, the collapse of related metallacycles in a HM cycle is probably rate-determining. It is therefore the relative energy barrier required for these steps that determines whether CM or HM is dominant with a particular complex.

Oxygen mediated oxidative couplings of flavones in alkaline water.

Catalyzed oxidative C-C bond coupling reactions play an important role in the chemical synthesis of complex natural products of medicinal importance. However, the poor functional group tolerance renders them unfit for the synthesis of naturally occurring polyphenolic flavones. We find that molecular oxygen in alkaline water acts as a hydrogen atom acceptor and oxidant in catalyst-free (without added catalyst) oxidative coupling of luteolin and other flavones. By this facile method, we achieve the synthesis of a small collection of flavone dimers and trimers including naturally occurring dicranolomin, philonotisflavone, dehydrohegoflavone, distichumtriluteolin, and cyclodistichumtriluteolin. Mechanistic studies using both experimental and computational chemistry uncover the underlying reasons for optimal pH, oxygen availability, and counter-cations that define the success of the reaction. We expect our reaction opens up a green and sustainable way to synthesize flavonoid dimers and oligomers using the readily available monomeric flavonoids isolated from biomass and exploiting their use for health care products and treatment of diseases.

Cap-binding complex assists RNA polymerase II transcription in plant salt stress response.

Adaptive response to stress involves an extensive reprogramming of gene expression. Under stressful conditions, the induction of efficient changes in messenger RNA (mRNA) production is crucial for maximized plant survival. Transcription and pre-mRNA processing are two closely related steps in mRNA biogenesis, yet how they are controlled in plant stress response remains elusive. Here, we show that the Arabidopsis nuclear cap-binding complex (CBC) component CBP20 directly interacts with ELF7, a subunit of the transcription elongation factor RNA Pol II-associated factor 1 complex (PAF1c) to promote RNA Pol II transcription in plant response to salt stress. CBP20 and ELF7 coregulate the expression of a large number of genes including those crucial for salt tolerance. Both CBP20 and ELF7 are required for enhanced RNA Pol II elongation at salt-activated genes. Though CBP20 also regulates intron splicing, this function is largely independent of ELF7. Our study reveals the function of an RNA processing regulator CBC in assisting efficient RNA Pol II transcription and pinpoints the complex roles of CBC on mRNA production in plant salt stress resistance.

A Diazo-Hooker Reaction, Inspired by the Biosynthesis of Azamerone.

Motivated by the biosynthesis of azamerone, we report the first example of a diazo-Hooker reaction, which involves the formation of a phthalazine ring system by the oxidative rearrangement of a diazoketone. Computational studies indicate that the diazo-Hooker reaction proceeds via an 8π-electrocyclization followed by ring contraction and aromatization. The biosynthetic origin of the diazoketone functional group was also chemically mimicked using a related natural product, naphterpin, as a model system.

π-Facial Stereoselectivity in Acyl Nitroso Cycloadditions to 5,5-Unsymmetrically Substituted Cyclopentadienes: Computational Exploration of Origins of Selectivity and the Role of Substituent Conformations on Selectivity.

The π-facial selectivity of Diels-Alder cycloadditions of 5-monosubstituted cyclopentadienes is known experimentally and has been extensively studied computationally. Previous studies on 5-monosubstituted cyclopentadienes by the Burnell and Houk groups showed that facial selectivity arises principally from hyperconjugative aromaticity or antiaromaticity of polar groups that cause distortion of the cyclopentadiene; steric effects of nonpolar groups can also be important. We have now explored the stereoselective cycloaddition of 5,5-unsymmetrically substituted cyclopentadienes to an acyl nitroso dienophile reported by Kan and co-workers. Computational studies with M06-2X/6-311+G(d,p) indicate that the stereoselectivity in the cycloadditions of 5,5-unsymmetrically substituted cyclopentadienes is not just a simple combination of effects found for monosubstituted counterparts. Substituent conformations and diene-dienophile steric and electronic interaction effects all influence stereoselectivity. Predictions are made about several as-yet-unstudied cyclopentadiene cycloadditions.

Cross-metathesis of Allenes. Mechanistic Analysis and Identification of a Ru-CAAC as the Most Effective Catalyst.

The first examples of cross-metathesis between two different allenes is disclosed. First- and second-generation Ru complexes were found to be ineffective, at most affording only oligomeric products. The exception was a first-generation complex bearing a bidentate phenyl isopropoxy ligand (i.e., PCy3 is not released upon initiation), reactions with which afforded a 1,3-disubstituted allenyl boronate in 22% yield. On the basis of mechanistic studies designed to gain deeper understanding of the reasons for the ineffectiveness of different Ru catalysts, it was discovered that phosphine-free Ru-CAAC complexes have the steric and electronic attributes to be highly effective. The results of these investigations pave the way for development of additional olefin metathesis reactions that generate allenes.

The histone variant H3.3 promotes the active chromatin state to repress flowering in Arabidopsis.

The histone H3 family in animals and plants includes replicative H3 and nonreplicative H3.3 variants. H3.3 preferentially associates with active transcription, yet its function in development and transcription regulation remains elusive. The floral transition in Arabidopsis (Arabidopsis thaliana) involves complex chromatin regulation at a central flowering repressor FLOWERING LOCUS C (FLC). Here, we show that H3.3 upregulates FLC expression and promotes active histone modifications histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 36 trimethylation (H3K36me3) at the FLC locus. The FLC activator FRIGIDA (FRI) directly mediates H3.3 enrichment at FLC, leading to chromatin conformation changes and further induction of active histone modifications at FLC. Moreover, the antagonistic H3.3 and H2A.Z act in concert to activate FLC expression, likely by forming unstable nucleosomes ideal for transcription processing. We also show that H3.3 knockdown leads to H3K4me3 reduction at a subset of particularly short genes, suggesting the general role of H3.3 in promoting H3K4me3. The finding that H3.3 stably accumulates at FLC in the absence of H3K36me3 indicates that the H3.3 deposition may serve as a prerequisite for active histone modifications. Our results reveal the important function of H3.3 in mediating the active chromatin state for flowering repression.

Computational determination of the mechanism of the Pd-catalyzed formation of isatoic anhydrides from o-haloanilines, CO, and CO2.

The palladium-catalyzed annulation of o-haloanilines with carbon monoxide (CO) and carbon dioxide (CO2), discovered by Wen-Zhen Zhang and co-workers, provides a convenient method to synthesize isatoic anhydrides. We explored the mechanism of this reaction, particularly the order of the reaction of CO and CO2 and the effect of the base, using density functional theory (DFT) calculations (ωB97X-D and M06). It was found that the base-assisted N-H bond activation through a concerted metalation-deprotonation (CMD) mechanism is a requisite for carboxylation, and the carboxylation proceeds via the nucleophilic attack of the (Pd)NH nitrogen on CO2. The results show that carbonylation occurs prior to carboxylation, because the facile and exergonic carbonylation greatly decreases the energies of the following intermediates and transition states. The mechanistic exploration of the alternative pathways (e.g., mono-carbonylation and carboxylation) and the comparison with the annulation mechanism of the o-iodobenzylamine substrate further demonstrate the perfect cooperation of CO and CO2 in constructing an anhydride moiety for o-haloanilines.

The INO80 chromatin remodeling complex promotes thermomorphogenesis by connecting H2A.Z eviction and active transcription in Arabidopsis.

Global warming poses a major threat to plant growth and crop production. In some plants, including Arabidopsis thaliana, elevated temperatures induce a series of morphological and developmental adjustments termed thermomorphogenesis, which facilitates plant cooling under high-temperature conditions. Plant thermal response is suppressed by histone variant H2A.Z. At warm temperatures, H2A.Z is evicted from nucleosomes at thermoresponsive genes, resulting in changes in their expression. However, the mechanisms that regulate H2A.Z eviction and subsequent transcriptional changes are largely unknown. Here, we show that the INO80 chromatin remodeling complex (INO80-C) promotes thermomorphogenesis and activates the expression of thermoresponsive and auxin-related genes. INO80-C associates with PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), a potent regulator of thermomorphogenesis, and mediates temperature-induced H2A.Z eviction at PIF4 targets. Moreover, INO80-C directly interacts with COMPASS-like and transcription elongation factors to promote active histone modification, histone H3 lysine 4 trimethylation, and RNA polymerase II elongation, leading to the thermal induction of transcription. Notably, the transcription elongation factors SPT4 and SPT5 are required for H2A.Z eviction at PIF4 targets, suggesting the cooperation of INO80-C and transcription elongation in H2A.Z removal. Taken together, these results suggest that the (PIF4)-(INO80-C)-(COMPASS-like)-(transcription elongator) module controls plant thermal response, thereby establishing a link between H2A.Z eviction and active transcription.

Diversification of Nucleophile-Intercepted Beckmann Fragmentation Products and Related Density Functional Theory Studies.

The nucleophile-intercepted Beckmann fragmentation (NuBFr) has the potential to be broadly applicable to the synthesis of indoline alkaloid-based natural products. However, the reaction has not been widely adopted, in part, because of limitations associated with the availability of appropriate promoter-Nu reagents. We have devised a stereospecific Ag(I)-promoted reaction for functionalizing NuBFr products to give novel compositions of matter that may be useful in synthesis and medicinal chemistry. With unhindered amine nucleophiles, structurally unique [2.2.2]-bicycloamidines are generated. We also disclose for the first time detailed density functional theory studies, which shed light on the mechanism of the NuBFr and Ag-promoted substitution reaction that supports an unusual aziridinium ion as a key intermediate.

High-Performance P2-Na0.70Mn0.80Co0.15Zr0.05O2 Cathode for Sodium-Ion Batteries.

Room-temperature sodium-ion batteries (NIBs) using a manganese-based layered cathode have been considered promising candidates for grid-scale energy storage applications. However, manganese-based materials suffer from serious Jahn-Teller distortion, phase transition, and unstable interface, resulting in severe structure degradation, sluggish sodium diffusion kinetics, and poor cycle, respectively. Herein, we demonstrate a Zr-doped Na0.70Mn0.80Co0.15Zr0.05O2 material with much improved specific capacity and rate capability compared with Zr-free Na0.70Mn0.85Co0.15O2 when used as cathode materials for NIBs. The material delivers a reversible capacity of 173 mA h g-1 at 0.1 C rate, corresponding to approximately 72% of the theoretical capacity (239 mA h g-1) based on a single-electron redox process, and a capacity retention of 88% after 50 cycles was obtained. Additionally, a homogenous solid-state interphase (SEI) film was revealed directly by high-resolution transmission electron microscopy in Zr-doped material after battery cycling. Electrochemical impedance spectroscopy proves that the formation of SEI films provides the Zr-doped material with special chemical/electrochemical stability. These results here give clear evidence of the utility of Zr-doping to improve the surface and environmental stability, sodium diffusion kinetics, and electrochemical performance of P2-type layered structure, promising advanced sodium-ion batteries with higher energy density, higher surface stability, and longer cycle life compared with the commonly used magnesiumdoping method in electrode materials.

Transcriptomic analysis of differentially expressed genes in flower-buds of genetic male sterile and wild type cucumber by RNA sequencing.

Cucumber (Cucumis sativus L.) pollen development involves a diverse range of gene interactions between sporophytic and gametophytic tissues. Previous studies in our laboratory showed that male sterility was controlled by a single recessive nuclear gene, and occurred in pollen mother cell meiophase. To fully explore the global gene expression and identify genes related to male sterility, a RNA-seq analysis was adopted in this study. Young male flower-buds (1-2 mm in length) from genetic male sterility (GMS) mutant and homozygous fertile cucumber (WT) were collected for two sequencing libraries. Total 545 differentially expressed genes (DEGs), including 142 up-regulated DEGs and 403 down-regulated DEGs, were detected in two libraries (Fold Change ≥ 2, FDR < 0.01). These genes were involved in a variety of metabolic pathways, like ethylene-activated signaling pathway, sporopollenin biosynthetic pathway, cell cycle and DNA damage repair pathway. qRT-PCR analysis was performed and showed that the correlation between RNA-Seq and qRT-PCR was 0.876. These findings contribute to a better understanding of the mechanism that leads to GMS in cucumber.

Fine mapping of a male sterility gene ms-3 in a novel cucumber (Cucumis sativus L.) mutant.

KEY MESSAGE: The cucumber male sterility gene ms - 3 was fine mapped in a 76 kb region harboring an MMD1 -like gene Csa3M006660 that may be responsible for the male sterile in cucumber. A cucumber (Cucumis sativus L.) male sterile mutant (ms-3) in an advanced-generation inbred line was identified, and genetic analysis revealed that the male sterility trait was controlled by a recessive nuclear gene, ms-3, which was stably inherited. Histological studies suggested that the main cause of the male sterility was defective microsporogenesis, resulting in no tetrad or microspores being formed. Bulked segregant analysis (BSA) and genotyping of an F2 population of 2553 individuals were employed used to fine map ms-3, which was delimited to a 76 Kb region. In this region, a single non-synonymous SNP was found in the Csa3M006660 gene locus, which was predicted to result in an amino acid change. Quantitative RT-PCR analysis of Csa3M006660 was consistent with the fact that it plays a role in the early development of cucumber pollen. The protein encoded by Csa3M006660 is predicted to be homeodomain (PHD) finger protein, and the high degree of sequence conservation with homologs from a range of plant species further suggested the importance of the ms-3 non-synonymous mutation. The data presented here provide support for Csa3M006660 as the most likely candidate gene for Ms-3.

Mechanistic insights into the selective cyclization of indolines with alkynes and alkenes to produce six- and seven-membered 1,7-fused indolines via Rh(iii) catalysis: a theoretical study.

The coupling reaction mechanisms of the Rh(iii)-catalyzed redox-neutral C7-selective aryl C-H functionalization of indolines with alkynes and alkenes have been theoretically investigated with the aid of the density functional theory (DFT) calculations. Our calculation results indicate that the active catalyst in this system is the cationic species [Cp*Rh(OAc)]+ (2cat) instead of the neutral species Cp*Rh(OAc)2 (1cat). The origin of forming different products associated with using different coupling partners was also rationalized in detail. For the coupling reaction of N-methoxycarbamoyl-protected indoline (1a) with alkyl alkyne (4a), the electronic effect plays a dominant role and causes the six-membered ring product to be the main product. For the coupling reaction of 1a with aryl alkyne (2a), through the replacement of alkyl alkyne with aryl alkyne, the steric effect serves as a crucial factor, compared with the electronic effect, and leads to the main seven-membered ring product. For the coupling reaction of 1a with acrylate (6a), the chemoselectivity is dictated by the steric effect and electronic effect.