Binding by the Polycomb complex component BMI1 and H2A monoubiquitination shape local and long-range interactions in the Arabidopsis genome.

Three-dimensional (3D) chromatin organization is highly dynamic during development and seems to play a crucial role in regulating gene expression. Self-interacting domains, commonly called topologically associating domains (TADs) or compartment domains (CDs), have been proposed as the basic structural units of chromatin organization. Surprisingly, although these units have been found in several plant species, they escaped detection in Arabidopsis (Arabidopsis thaliana). Here, we show that the Arabidopsis genome is partitioned into contiguous CDs with different epigenetic features, which are required to maintain appropriate intra-CD and long-range interactions. Consistent with this notion, the histone-modifying Polycomb group machinery is involved in 3D chromatin organization. Yet, while it is clear that Polycomb repressive complex 2 (PRC2)-mediated trimethylation of histone H3 on lysine 27 (H3K27me3) helps establish local and long-range chromatin interactions in plants, the implications of PRC1-mediated histone H2A monoubiquitination on lysine 121 (H2AK121ub) are unclear. We found that PRC1, together with PRC2, maintains intra-CD interactions, but it also hinders the formation of H3K4me3-enriched local chromatin loops when acting independently of PRC2. Moreover, the loss of PRC1 or PRC2 activity differentially affects long-range chromatin interactions, and these 3D changes differentially affect gene expression. Our results suggest that H2AK121ub helps prevent the formation of transposable element/H3K27me1-rich long loops and serves as a docking point for H3K27me3 incorporation.

Photobiocatalytic Strategies for Organic Synthesis.

Biocatalysis has revolutionized chemical synthesis, providing sustainable methods for preparing various organic molecules. In enzyme-mediated organic synthesis, most reactions involve molecules operating from their ground states. Over the past 25 years, there has been an increased interest in enzymatic processes that utilize electronically excited states accessed through photoexcitation. These photobiocatalytic processes involve a diverse array of reaction mechanisms that are complementary to one another. This comprehensive review will describe the state-of-the-art strategies in photobiocatalysis for organic synthesis until December 2022. Apart from reviewing the relevant literature, a central goal of this review is to delineate the mechanistic differences between the general strategies employed in the field. We will organize this review based on the relationship between the photochemical step and the enzymatic transformations. The review will include mechanistic studies, substrate scopes, and protein optimization strategies. By clearly defining mechanistically-distinct strategies in photobiocatalytic chemistry, we hope to illuminate future synthetic opportunities in the area.

SlPPDK modulates sugar and acid metabolism to influence flavor quality during tomato fruit ripening.

Fruit ripening is a highly intricate process, where the dynamic interplay of soluble sugar and organic acid metabolism is crucial for developing the characteristic flavor qualities. Pyruvate orthophosphate dikinase (PPDK) plays a pivotal role in modulating the process of gluconeogenesis during plant development. However, the specific physiological role of PPDK in fruit development has yet to be elucidated. In this study, we investigated the expression pattern, subcellular localization and functional significance of SlPPDK in tomato fruits. Our results reveal that SlPPDK is highly expressed in fruits and flowers, with its expression progressively increasing as the fruit ripens. Subcellular localization analyses demonstrate that SlPPDK is distributed in the cell membrane, cytoplasm, and nucleus. Using CRISPR/Cas9 technology, we generated SlPPDK knockout mutants, which exhibited a marked reduction in enzyme activity, leading to significant alterations in sugar and organic acid metabolism. These findings highlight the critical role of SlPPDK in maintaining the sugar-acid balance essential for tomato flavor quality and provide a foundation for future breeding strategies aimed at enhancing tomato fruit flavor.

De novo centromere formation in pericentromeric region of rice chromosome 8.

Neocentromeres develop when kinetochores assemble de novo at DNA loci that are not previously associated with CenH3 nucleosomes, and can rescue rearranged chromosomes that have lost a functional centromere. The molecular mechanisms associated with neocentromere formation in plants have been elusive. Here, we developed a Xian (indica) rice line with poor growth performance in the field due to approximately 272 kb deletion that spans centromeric DNA sequences, including the centromeric satellite repeat CentO, in the centromere of chromosome 8 (Cen8). The CENH3-binding domains were expanded downstream of the original CentO position in Cen8, which revealed a de novo centromere formation in rice. The neocentromere formation avoids chromosomal regions containing functional genes. Meanwhile, canonical histone H3 was replaced by CENH3 in the regions with low CENH3 levels, and the CenH3 nucleosomes in these regions became more periodic. In addition, we identified active genes in the deleted centromeric region, which are essential for chloroplast growth and development. In summary, our results provide valuable insights into neocentromere formation and show that functional genes exist in the centromeric regions of plant chromosomes.

Histone deacetylase OsHDA706 increases salt tolerance via H4K5/K8 deacetylation of OsPP2C49 in rice.

High salt is a major environmental factor that threatens plant growth and development. Increasing evidence indicates that histone acetylation is involved in plant responses to various abiotic stress; however, the underlying epigenetic regulatory mechanisms remain poorly understood. In this study, we revealed that the histone deacetylase OsHDA706 epigenetically regulates the expression of salt stress response genes in rice (Oryza sativa L.). OsHDA706 localizes to the nucleus and cytoplasm and OsHDA706 expression is significantly induced under salt stress. Moreover, oshda706 mutants showed a higher sensitivity to salt stress than the wild-type. In vivo and in vitro enzymatic activity assays demonstrated that OsHDA706 specifically regulates the deacetylation of lysines 5 and 8 on histone H4 (H4K5 and H4K8). By combining chromatin immunoprecipitation and mRNA sequencing, we identified the clade A protein phosphatase 2 C gene, OsPP2C49, which is involved in the salt response as a direct target of H4K5 and H4K8 acetylation. We found that the expression of OsPP2C49 is induced in the oshda706 mutant under salt stress. Furthermore, the knockout of OsPP2C49 enhances plant tolerance to salt stress, while its overexpression has the opposite effect. Taken together, our results indicate that OsHDA706, a histone H4 deacetylase, participates in the salt stress response by regulating the expression of OsPP2C49 via H4K5 and H4K8 deacetylation.

Enantioselective Deaminative Alkylation of Amino Acid Derivatives with Unactivated Olefins.

Herein, we report the first Ni-catalyzed enantioselective deaminative alkylation of amino acid and peptide derivatives with unactivated olefins. Key for success was the discovery of a new sterically encumbered bis(oxazoline) ligand backbone, thus offering a de novo technology for accessing enantioenriched sp3-sp3 linkages via sp3 C-N functionalization. Our protocol is distinguished by its broad scope and generality across a wide number of counterparts, even in the context of late-stage functionalization. In addition, an enantioselective deaminative remote hydroalkylation reaction of unactivated internal olefins is within reach, thus providing a useful entry point for forging enantioenriched sp3-sp3 centers at remote sp3 C-H sites.

Dual-color oligo-FISH can reveal chromosomal variations and evolution in Oryza species.

Fluorescence in situ hybridization using probes based on oligonucleotides (oligo-FISH) is a useful tool for chromosome identification and karyotype analysis. Here we developed two oligo-FISH probes that allow the identification of each of the 12 pairs of chromosomes in rice (Oryza sativa). These two probes comprised 25 717 (green) and 25 215 (red) oligos (45 nucleotides), respectively, and generated 26 distinct FISH signals that can be used as a barcode to uniquely label each of the 12 pairs of rice chromosomes. Standard karyotypes of rice were established using this system on both mitotic and meiotic chromosomes. Moreover, dual-color oligo-FISH was used to characterize diverse chromosomal abnormalities. Oligo-FISH analyses using these probes in various wild Oryza species revealed that chromosomes from the AA, BB or CC genomes generated specific and intense signals similar to those in rice, while chromosomes with the EE genome generated less specific signals and the FF genome gave no signal. Together, the oligo-FISH probes we established will be a powerful tool for studying chromosome variations and evolution in the genus Oryza.

Molecular mechanisms of heavy metals resistance of Stenotrophomonas rhizophila JC1 by whole genome sequencing.

In this study, a higher metal ions-resistant bacterium, Stenotrophomonas rhizophila JC1 was isolated from contaminated soil in Jinchang city, Gansu Province, China. The Pb2+ (120 mg/L) and Cu2+ (80 mg/L) removal rate of the strain reached at 76.9% and 83.4%, respectively. The genome comprises 4268161 bp in a circular chromosome with 67.52% G + C content and encodes 3719 proteins. The genome function analysis showed czc operon, mer operon, cop operon, arsenic detoxification system in strain JC1 were contributed to the removal of heavy metals. Three efflux systems (i.e., RND, CDF, and P-ATPase) on strain JC1 genome could trigger the removal of divalent cations from cells. cAMP pathway and ABC transporter pathway might be involved in the transport and metabolism of heavy metals. The homology analysis exhibited multi-gene families such as ABC transporters, heavy metal-associated domain, copper resistance protein, carbohydrate-binding domain were distributed across 410 orthologous groups. In addition, heavy metal-responsive transcription regulator, thioredoxin, heavy metal transport/detoxification protein, divalent-cation resistance protein CutA, arsenate reductase also played important roles in the heavy metals adsorption and detoxification process. The complete genome data provides insight into the exploration of the interaction mechanism between microorganisms and heavy metals.

Cellular alterations and crosstalk in the osteochondral joint in osteoarthritis and promising therapeutic strategies.

Osteoarthritis (OA) is a joint disorder involving cartilage degeneration and subchondral bone sclerosis. The bone-cartilage interface is implicated in OA pathogenesis due to its susceptibility to mechanical and biological factors. The crosstalk between cartilage and the underlying subchondral bone is elevated in OA due to multiple factors, such as increased vascularization, porosity, microcracks and fissures. Changes in the osteochondral joint are traceable to alterations in chondrocytes and bone cells (osteoblasts, osteocytes and osteoclasts). The phenotypes of these cells can change with the progression of OA. Aberrant intercellular communications among bone cell-bone cell and bone cell-chondrocyte are of great importance and might be the factors promoting OA development. An appreciation of cellular phenotypic changes in OA and the mechanisms by which these cells communicate would be expected to lead to the development of targeted drugs with fewer side effects.

Pseudomonas quercus sp. nov, associated with leaf spot disease of Quercus mongolica.

Two Gram-negative, aerobic, motile bacteria strains were isolated from leaf spot disease of Quercus mongolica. Strain hsmgli-8T has 99.86 % 16S rRNA gene sequence similarity to LY10J, and the highest 16S rRNA gene sequence similarity to Pseudomonas cerasi 58T (97.2 %), then Pseudomonas ficuserectae JCM 2400T (97.18 %), Pseudomonas meliae CFBP 3225T, Pseudomonas tremae CFBP 6111T and Pseudomonas congelans DSM 14939T (all 97.12 %), and less than 97.1 % similarity to other recognized species. In phylogenetic trees based on 16S rRNA gene and multilocus sequence data, the two novel strains form a separate branch, indicating that they do not belong to any Pseudomonas group and subgroup, and should belong to a novel species within the genus Pseudomonas. This assertion is also supported by the results of genome average nucleotide identity analysis. The major fatty acids are C16 : 0, C18 : 1 ω7c and/or C18 : 1 ω6c, C16 : 1 ω7c and/or C16 : 1 ω6c. Polar lipids include phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, aminolipid and seven uncharacterized phospholipids. The predominant respiratory quinone is Q-9. The DNA G+C content is 59.45-59.50 mol%. Based on these data, we propose that the two novel strains should be assigned as a novel species within the genus Pseudomonas. We propose that the novel strains be named Pseudomonas quercus sp. nov. The type strain is hsmgli-8T (=CFCC 15739T=LMG 31544T).

sp3 Bis-Organometallic Reagents via Catalytic 1,1-Difunctionalization of Unactivated Olefins.

A catalytic 1,1-difunctionalization of unactivated olefins en route to sp3 bis-organometallic B,B(Si)-reagents is described. The protocol is characterized by exceptional reaction rates, mild conditions, wide scope, and exquisite selectivity pattern, constituting a new platform to access sp3 bis-organometallics.

Site-Selective 1,2-Dicarbofunctionalization of Vinyl Boronates through Dual Catalysis.

A modular, site-selective 1,2-dicarbofunctionalization of vinyl boronates with organic halides through dual catalysis is described. This reaction proceeds under mild conditions and is characterized by excellent chemo- and regioselectivity. It thus represents a complementary new technique for preparing densely functionalized alkyl boron architectures from simple and accessible precursors.

Cascade One-Pot Synthesis of Orange-Red-Fluorescent Polycyclic Cinnolino[2,3-f]phenanthridin-9-ium Salts by Palladium(II)-Catalyzed C-H Bond Activation of 2-Azobiaryl Compounds and Alkenes.

Quaternary ammonium salts were synthesized in moderate to good yields through double oxidative C-H bond activation on azobenzenes. The mechanism of the highly regioselective reaction of 2-azobiaryls with alkenes to give orange-red-fluorescent cinnolino[2,3-f]phenanthridin-9-ium salts and 15H-cinnolino[2,3-f]phenanthridin-9-ium-10-ide is proposed to involve ortho C-H olefination of the 2-azobiaryl compound with the alkene, intramolecular aza-Michael addition, concerted metalation-deprotonation (CMD), reductive elimination, and oxidation.

Site-Selective Catalytic Deaminative Alkylation of Unactivated Olefins.

A catalytic deaminative alkylation of unactivated olefins is described. The protocol is characterized by its mild conditions, wide scope, including the use of ethylene as substrate, and exquisite site-selectivity pattern for both α-olefins and internal olefins, thus unlocking a new catalytic platform to forge sp3-sp3 linkages, even in the context of late-stage functionalization.

Site-Selective Ni-Catalyzed Reductive Coupling of α-Haloboranes with Unactivated Olefins.

A mild, chemo- and site-selective catalytic protocol that allows for incorporating an alkylboron fragment into unactivated olefins is described. The use of internal olefins enables C-C bond-formation at remote sp3 C-H sites, constituting a complementary and conceptually different approach to existing borylation techniques that are currently available at sp3 centers.

Nickel-Catalyzed Umpolung Arylation of Ambiphilic α-Bromoalkyl Boronic Esters.

A nickel-catalyzed reductive arylation of ambiphilic α-bromoalkyl boronic esters with aryl halides is described. This platform provides an unrecognized opportunity to promote the catalytic umpolung reactivity of ambiphilic reagents with aryl halides, thus unlocking a new cross-coupling strategy that complements existing methods for the preparation of densely functionalized alkyl-substituted organometallic reagents from simple and readily accessible precursors.

Integrated photonic power divider with arbitrary power ratios.

Integrated optical power splitters are one of the fundamental building blocks in photonic integrated circuits. Conventional multimode interferometer-based power splitters are widely used as they have reasonable footprints and are easy to fabricate. However, it is challenging to realize arbitrary split ratios, especially for multi-outputs. In this Letter, an ultra-compact power splitter with a QR code-like nanostructure is designed by a nonlinear fast search method. The highly functional structure is composed of a number of freely designed square pixels with the size of 120×120 nm which could be either dielectric or air. The light waves are scattered by a number of etched squares with optimized locations, and the scattered waves superimpose at the outputs with the desired power ratio. We demonstrate 1×2 splitters with 1:1, 1:2, and 1:3 split ratios, and a 1×3 splitter with the ratio of 1:2:1. The footprint for all the devices is only 3.6×3.6 µm. Well-controlled split ratios are measured for all the cases. The measured transmission efficiencies of all the splitters are close to 80% over 30 nm wavelength range.

Switchable Site-Selective Catalytic Carboxylation of Allylic Alcohols with CO2.

A switchable site-selective catalytic carboxylation of allylic alcohols has been developed in which CO2 is used with dual roles, both facilitating C-OH cleavage and as a C1 source. This protocol is characterized by its mild reaction conditions, absence of stoichiometric amounts of organometallic reagents, broad scope, and exquisite regiodivergency which can be modulated by the type of ligand employed.

Cu(II)-Mediated C(sp(2))-H Hydroxylation.

A Cu(II)-mediated ortho-C-H hydroxylation using a removable directing group has been developed. The reaction exhibits considerable functional group tolerance. The use of O2 as an oxidant is crucial for the reactivity. Water is also found to significantly improve this reaction.

Cu(II)-mediated C-H amidation and amination of arenes: exceptional compatibility with heterocycles.

A Cu(OAc)2-mediated C-H amidation and amination of arenes and heteroarenes has been developed using a readily removable directing group. A wide range of sulfonamides, amides, and anilines function as amine donors in this reaction. Heterocycles present in both reactants are tolerated, making this a broadly applicable method for the synthesis of a family of inhibitors including 2-benzamidobenzoic acids and N-phenylaminobenzoates.