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1.
Cell ; 174(4): 818-830.e11, 2018 08 09.
Article in English | MEDLINE | ID: mdl-30057113

ABSTRACT

Rtt109 is a unique histone acetyltransferase acetylating histone H3 lysine 56 (H3K56), a modification critical for DNA replication-coupled nucleosome assembly and genome stability. In cells, histone chaperone Asf1 is essential for H3K56 acetylation, yet the mechanisms for H3K56 specificity and Asf1 requirement remain unknown. We have determined the crystal structure of the Rtt109-Asf1-H3-H4 complex and found that unwinding of histone H3 αN, where K56 is normally located, and stabilization of the very C-terminal ß strand of histone H4 by Asf1 are prerequisites for H3K56 acetylation. Unexpectedly, an interaction between Rtt109 and the central helix of histone H3 is also required. The observed multiprotein, multisite substrate recognition mechanism among histone modification enzymes provides mechanistic understandings of Rtt109 and Asf1 in H3K56 acetylation, as well as valuable insights into substrate recognition by histone modification enzymes in general.


Subject(s)
Aspergillus fumigatus/metabolism , Histone Acetyltransferases/metabolism , Histones/chemistry , Lysine/metabolism , Molecular Chaperones/metabolism , Acetylation , Amino Acid Sequence , Histone Acetyltransferases/chemistry , Histones/metabolism , Lysine/chemistry , Molecular Chaperones/chemistry , Protein Conformation , Saccharomyces cerevisiae/growth & development , Saccharomyces cerevisiae/metabolism , Sequence Homology , Substrate Specificity
2.
Nature ; 615(7953): 634-639, 2023 03.
Article in English | MEDLINE | ID: mdl-36859552

ABSTRACT

The selective conversion of natural or synthetic neral to (1R,6S)-trans-isopiperitenol would enable and expedite sustainable routes to menthol1,2 and cannabinoids3-5. However, this reaction has been considered impossible because its product is more reactive to the required acid catalysts than its starting material, resulting in several side products6-9. We now show that an unsymmetric, strong and confined chiral acid, a highly fluorinated imino-imidodiphosphate, catalyses this process with excellent efficiency and selectivity. Expanding the method to other α,ß-unsaturated aldehydes could enable access to new cannabinoids and menthol derivatives not readily accessible previously. Mechanistic studies suggest that the confined catalyst accomplishes this reaction by binding the product in an unreactive conformation, thereby preventing its decomposition. We also show how (1R,6S)-trans-isopiperitenol can be readily converted to pharmaceutically useful cannabinoids and menthol, each in the shortest and most atom-economic routes so far.


Subject(s)
Acyclic Monoterpenes , Cannabinoids , Catalysis , Chemistry Techniques, Synthetic , Menthol , Cannabinoids/chemical synthesis , Cannabinoids/chemistry , Menthol/analogs & derivatives , Menthol/chemical synthesis , Menthol/chemistry , Aldehydes/chemistry , Halogenation , Acyclic Monoterpenes/chemistry
3.
Nature ; 614(7946): 75-80, 2023 02.
Article in English | MEDLINE | ID: mdl-36725995

ABSTRACT

Time-periodic light field has emerged as a control knob for manipulating quantum states in solid-state materials1-3, cold atoms4 and photonic systems5 through hybridization with photon-dressed Floquet states6 in the strong-coupling limit, dubbed Floquet engineering. Such interaction leads to tailored properties of quantum materials7-11, for example, modifications of the topological properties of Dirac materials12,13 and modulation of the optical response14-16. Despite extensive research interests over the past decade3,8,17-20, there is no experimental evidence of momentum-resolved Floquet band engineering of semiconductors, which is a crucial step to extend Floquet engineering to a wide range of solid-state materials. Here, on the basis of time and angle-resolved photoemission spectroscopy measurements, we report experimental signatures of Floquet band engineering in a model semiconductor, black phosphorus. On near-resonance pumping at a photon energy of 340-440 meV, a strong band renormalization is observed near the band edges. In particular, light-induced dynamical gap opening is resolved at the resonance points, which emerges simultaneously with the Floquet sidebands. Moreover, the band renormalization shows a strong selection rule favouring pump polarization along the armchair direction, suggesting pseudospin selectivity for the Floquetband engineering as enforced by the lattice symmetry. Our work demonstrates pseudospin-selective Floquet band engineering in black phosphorus and provides important guiding principles for Floquet engineering of semiconductors.

4.
Nature ; 623(7987): 643-651, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37938774

ABSTRACT

In eukaryotes, repetitive DNA sequences are transcriptionally silenced through histone H3 lysine 9 trimethylation (H3K9me3). Loss of silencing of the repeat elements leads to genome instability and human diseases, including cancer and ageing1-3. Although the role of H3K9me3 in the establishment and maintenance of heterochromatin silencing has been extensively studied4-6, the pattern and mechanism that underlie the partitioning of parental H3K9me3 at replicating DNA strands are unknown. Here we report that H3K9me3 is preferentially transferred onto the leading strands of replication forks, which occurs predominantly at long interspersed nuclear element (LINE) retrotransposons (also known as LINE-1s or L1s) that are theoretically transcribed in the head-on direction with replication fork movement. Mechanistically, the human silencing hub (HUSH) complex interacts with the leading-strand DNA polymerase Pol ε and contributes to the asymmetric segregation of H3K9me3. Cells deficient in Pol ε subunits (POLE3 and POLE4) or the HUSH complex (MPP8 and TASOR) show compromised H3K9me3 asymmetry and increased LINE expression. Similar results were obtained in cells expressing a MPP8 mutant defective in H3K9me3 binding and in TASOR mutants with reduced interactions with Pol ε. These results reveal an unexpected mechanism whereby the HUSH complex functions with Pol ε to promote asymmetric H3K9me3 distribution at head-on LINEs to suppress their expression in S phase.


Subject(s)
Gene Silencing , Histones , Long Interspersed Nucleotide Elements , Lysine , S Phase , Humans , DNA Replication , Histones/chemistry , Histones/metabolism , Long Interspersed Nucleotide Elements/genetics , Lysine/metabolism , Methylation
5.
Cell ; 155(4): 817-29, 2013 Nov 07.
Article in English | MEDLINE | ID: mdl-24209620

ABSTRACT

Nucleosome assembly following DNA replication and gene transcription is important to maintain genome stability and epigenetic information. Newly synthesized histones H3-H4 first bind histone chaperone Asf1 and are then transferred to other chaperones for nucleosome assembly. However, it is unknown how H3-H4 is transferred from the Asf1-H3-H4 complex to other chaperones because Asf1 binds H3-H4 with high affinity. Here, we show that yeast Rtt101(Mms1) E3 ubiquitin ligase preferentially binds and ubiquitylates new histone H3 acetylated at lysine 56. Inactivation of Rtt101 or mutating H3 lysine residues ubiquitylated by the Rtt101(Mms1) ligase impairs nucleosome assembly and promotes Asf1-H3 interactions. Similar phenotypes occur in human cells in which the ortholog of Rtt101(Mms1), Cul4A(DDB1), is depleted. These results indicate that the transfer of H3-H4 from the Asf1-H3-H4 complex to other histone chaperones is regulated by a conserved E3 ligase and provide evidence for crosstalk between histone acetylation and ubiquitylation in nucleosome assembly.


Subject(s)
Cullin Proteins/metabolism , Histones/metabolism , Nucleosomes/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomycetales/metabolism , Acetylation , Cell Cycle Proteins/metabolism , Cullin Proteins/chemistry , Humans , Models, Molecular , Molecular Chaperones/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Ubiquitination
6.
Nature ; 605(7908): 84-89, 2022 05.
Article in English | MEDLINE | ID: mdl-35508776

ABSTRACT

Enzymatic stereoselectivity has typically been unrivalled by most chemical catalysts, especially in the conversion of small substrates. According to the 'lock-and-key theory'1,2, enzymes have confined active sites to accommodate their specific reacting substrates, a feature that is typically absent from chemical catalysts. An interesting case in this context is the formation of cyanohydrins from ketones and HCN, as this reaction can be catalysed by various classes of catalysts, including biological, inorganic and organic ones3-7. We now report the development of broadly applicable confined organocatalysts for the highly enantioselective cyanosilylation of aromatic and aliphatic ketones, including the challenging 2-butanone. The selectivity (98:2 enantiomeric ratio (e.r.)) obtained towards its pharmaceutically relevant product is unmatched by any other catalyst class, including engineered biocatalysts. Our results indicate that confined chemical catalysts can be designed that are as selective as enzymes in converting small, unbiased substrates, while still providing a broad scope.


Subject(s)
Ketones , Catalysis , Ketones/chemistry , Stereoisomerism
7.
Nature ; 599(7884): 256-261, 2021 11.
Article in English | MEDLINE | ID: mdl-34707286

ABSTRACT

The identity of the earliest inhabitants of Xinjiang, in the heart of Inner Asia, and the languages that they spoke have long been debated and remain contentious1. Here we present genomic data from 5 individuals dating to around 3000-2800 BC from the Dzungarian Basin and 13 individuals dating to around 2100-1700 BC from the Tarim Basin, representing the earliest yet discovered human remains from North and South Xinjiang, respectively. We find that the Early Bronze Age Dzungarian individuals exhibit a predominantly Afanasievo ancestry with an additional local contribution, and the Early-Middle Bronze Age Tarim individuals contain only a local ancestry. The Tarim individuals from the site of Xiaohe further exhibit strong evidence of milk proteins in their dental calculus, indicating a reliance on dairy pastoralism at the site since its founding. Our results do not support previous hypotheses for the origin of the Tarim mummies, who were argued to be Proto-Tocharian-speaking pastoralists descended from the Afanasievo1,2 or to have originated among the Bactria-Margiana Archaeological Complex3 or Inner Asian Mountain Corridor cultures4. Instead, although Tocharian may have been plausibly introduced to the Dzungarian Basin by Afanasievo migrants during the Early Bronze Age, we find that the earliest Tarim Basin cultures appear to have arisen from a genetically isolated local population that adopted neighbouring pastoralist and agriculturalist practices, which allowed them to settle and thrive along the shifting riverine oases of the Taklamakan Desert.


Subject(s)
Archaeology , Genome, Human/genetics , Genomics , Human Migration/history , Mummies/history , Phylogeny , Agriculture/history , Animals , Cattle , China , Cultural Characteristics , Dental Calculus/chemistry , Desert Climate , Diet/history , Europe , Female , Goats , Grassland , History, Ancient , Humans , Male , Milk Proteins/analysis , Phylogeography , Principal Component Analysis , Proteome/analysis , Proteomics , Sheep , Whole Genome Sequencing
8.
Immunity ; 46(6): 992-1004.e5, 2017 06 20.
Article in English | MEDLINE | ID: mdl-28636969

ABSTRACT

RNA interference (RNAi) functions as a potent antiviral immunity in plants and invertebrates; however, whether RNAi plays antiviral roles in mammals remains unclear. Here, using human enterovirus 71 (HEV71) as a model, we showed HEV71 3A protein as an authentic viral suppressor of RNAi during viral infection. When the 3A-mediated RNAi suppression was impaired, the mutant HEV71 readily triggered the production of abundant HEV71-derived small RNAs with canonical siRNA properties in cells and mice. These virus-derived siRNAs were produced from viral dsRNA replicative intermediates in a Dicer-dependent manner and loaded into AGO, and they were fully active in degrading cognate viral RNAs. Recombinant HEV71 deficient in 3A-mediated RNAi suppression was significantly restricted in human somatic cells and mice, whereas Dicer deficiency rescued HEV71 infection independently of type I interferon response. Thus, RNAi can function as an antiviral immunity, which is induced and suppressed by a human virus, in mammals.


Subject(s)
Enterovirus A, Human/immunology , Enterovirus Infections/immunology , Immunity , RNA Interference , RNA, Viral/immunology , Animals , Argonaute Proteins/metabolism , Clustered Regularly Interspaced Short Palindromic Repeats , Enterovirus A, Human/genetics , HEK293 Cells , Humans , Mammals , Mice , Mice, 129 Strain , Mice, Knockout , Mutation/genetics , Ribonuclease III/metabolism , Viral Proteins/immunology
9.
Mol Cell ; 72(1): 140-151.e3, 2018 10 04.
Article in English | MEDLINE | ID: mdl-30244834

ABSTRACT

Although essential for epigenetic inheritance, the transfer of parental histone (H3-H4)2 tetramers that contain epigenetic modifications to replicating DNA strands is poorly understood. Here, we show that the Mcm2-Ctf4-Polα axis facilitates the transfer of parental (H3-H4)2 tetramers to lagging-strand DNA at replication forks. Mutating the conserved histone-binding domain of the Mcm2 subunit of the CMG (Cdc45-MCM-GINS) DNA helicase, which translocates along the leading-strand template, results in a marked enrichment of parental (H3-H4)2 on leading strand, due to the impairment of the transfer of parental (H3-H4)2 to lagging strands. Similar effects are observed in Ctf4 and Polα primase mutants that disrupt the connection of the CMG helicase to Polα that resides on lagging-strand template. Our results support a model whereby parental (H3-H4)2 complexes displaced from nucleosomes by DNA unwinding at replication forks are transferred by the CMG-Ctf4-Polα complex to lagging-strand DNA for nucleosome assembly at the original location.


Subject(s)
DNA Polymerase III/genetics , DNA Replication/genetics , DNA-Binding Proteins/genetics , Saccharomyces cerevisiae Proteins/genetics , Chromatin Assembly and Disassembly/genetics , DNA Helicases/genetics , Epigenesis, Genetic , Histones/genetics , Multiprotein Complexes/genetics , Nucleosomes/genetics , Protein Binding , Saccharomyces cerevisiae/genetics
10.
Proc Natl Acad Sci U S A ; 120(39): e2305078120, 2023 Sep 26.
Article in English | MEDLINE | ID: mdl-37695879

ABSTRACT

Current un-sustainable plastic management is exacerbating plastic pollution, an urgent shift is thus needed to create a recycling society. Such recovering carbon (C) and hydrogen (H) from waste plastic has been considered as one practical route to achieve a circular economy. Here, we performed a simple pyrolysis-catalysis deconstruction of waste plastic via a monolithic multilayer stainless-steel mesh catalyst to produce multiwalled carbon nanotubes (MWCNTs) and H2, which are important carbon material and energy carrier to achieve sustainable development. Results revealed that the C and H recovery efficiencies were as high as 86% and 70%, respectively. The unique oxidation-reduction process and improvement of surface roughness led to efficient exposure of active sites, which increased MWCNTs by suppressing macromolecule hydrocarbons. The C recovery efficiency declined by only 5% after 10 cycles, proving the long-term employment of the catalyst. This catalyst can efficiently convert aromatics to MWCNTs by the vapor-solid-solid mechanism and demonstrate good universality in processing different kinds of waste plastics. The produced MWCNTs showed potential in applications of lithium-ion batteries and telecommunication. Owing to the economic profits and environmental benefits of the developed route, we highlighted its potential as a promising alternative to conventional incineration, simultaneously achieving the waste-to-resource strategy and circular economy.

11.
Genome Res ; 32(6): 1026-1041, 2022 06.
Article in English | MEDLINE | ID: mdl-35609991

ABSTRACT

Polypeptides encoded by long noncoding RNAs (lncRNAs) are a novel class of functional molecules. However, whether these hidden polypeptides participate in the TP53 pathway and play a significant biological role is still unclear. Here, we discover that TP53-regulated lncRNAs can encode peptides, two of which are functional in various human cell lines. Using ribosome profiling and RNA-seq approaches in HepG2 cells, we systematically identified more than 300 novel TP53-regulated lncRNAs and further confirmed that 15 of these TP53-regulated lncRNAs encode peptides. Furthermore, several peptides were validated by mass spectrometry. Ten of the novel translational lncRNAs are directly inducible by TP53 in response to DNA damage. We show that the TP53-inducible peptides TP53LC02 and TP53LC04, but not their lncRNAs, can suppress cell proliferation. TP53LC04 peptide also has a function associated with cell proliferation by regulating the cell cycle in response to DNA damage. This study shows that TP53-regulated lncRNAs can encode new functional peptides, leading to the expansion of the TP53 tumor-suppressor network and providing novel potential targets for cancer therapy.


Subject(s)
RNA, Long Noncoding , Cell Proliferation/genetics , Humans , Peptides/metabolism , Peptides/pharmacology , RNA, Long Noncoding/metabolism , Ribosomes/metabolism , Tumor Suppressor Protein p53/genetics
12.
Plant Cell ; 34(5): 1890-1911, 2022 04 26.
Article in English | MEDLINE | ID: mdl-35166333

ABSTRACT

The unique morphology of grass stomata enables rapid responses to environmental changes. Deciphering the basis for these responses is critical for improving food security. We have developed a planta platform of single-nucleus RNA-sequencing by combined fluorescence-activated nuclei flow sorting, and used it to identify cell types in mature and developing stomata from 33,098 nuclei of the maize epidermis-enriched tissues. Guard cells (GCs) and subsidiary cells (SCs) displayed differential expression of genes, besides those encoding transporters, involved in the abscisic acid, CO2, Ca2+, starch metabolism, and blue light signaling pathways, implicating coordinated signal integration in speedy stomatal responses, and of genes affecting cell wall plasticity, implying a more sophisticated relationship between GCs and SCs in stomatal development and dumbbell-shaped guard cell formation. The trajectory of stomatal development identified in young tissues, and by comparison to the bulk RNA-seq data of the MUTE defective mutant in stomatal development, confirmed known features, and shed light on key participants in stomatal development. Our study provides a valuable, comprehensive, and fundamental foundation for further insights into grass stomatal function.


Subject(s)
Plant Stomata , Zea mays , Humans , Plant Leaves/metabolism , Plant Stomata/metabolism , Poaceae/genetics , Transcriptome/genetics , Zea mays/genetics
13.
Mol Cell ; 65(2): 272-284, 2017 Jan 19.
Article in English | MEDLINE | ID: mdl-28107649

ABSTRACT

The histone chaperone HIRA is involved in depositing histone variant H3.3 into distinct genic regions, including promoters, enhancers, and gene bodies. However, how HIRA deposits H3.3 to these regions remains elusive. Through a short hairpin RNA (shRNA) screening, we identified single-stranded DNA binding protein replication protein A (RPA) as a regulator of the deposition of newly synthesized H3.3 into chromatin. We show that RPA physically interacts with HIRA to form RPA-HIRA-H3.3 complexes, and it co-localizes with HIRA and H3.3 at gene promoters and enhancers. Depletion of RPA1, the largest subunit of the RPA complex, dramatically reduces both HIRA association with chromatin and the deposition of newly synthesized H3.3 at promoters and enhancers and leads to altered transcription at gene promoters. These results support a model whereby RPA, best known for its role in DNA replication and repair, recruits HIRA to promoters and enhancers and regulates deposition of newly synthesized H3.3 to these regulatory elements for gene regulation.


Subject(s)
Cell Cycle Proteins/metabolism , Chromatin/metabolism , DNA-Binding Proteins/metabolism , DNA/metabolism , Enhancer Elements, Genetic , Histone Chaperones/metabolism , Histones/metabolism , Promoter Regions, Genetic , Replication Protein A/metabolism , Transcription Factors/metabolism , Transcription, Genetic , Binding Sites , Cell Cycle Proteins/genetics , Chromatin/genetics , DNA/genetics , DNA-Binding Proteins/genetics , G1 Phase , HEK293 Cells , HeLa Cells , Histone Chaperones/genetics , Humans , Protein Binding , Protein Interaction Domains and Motifs , RNA Interference , Replication Protein A/genetics , Transcription Factors/genetics , Transfection
14.
Cell Mol Life Sci ; 81(1): 128, 2024 Mar 12.
Article in English | MEDLINE | ID: mdl-38472451

ABSTRACT

Epigenetic dysregulation that leads to alterations in gene expression and is suggested to be one of the key pathophysiological factors of Parkinson's disease (PD). Here, we found that α-synuclein preformed fibrils (PFFs) induced histone H3 dimethylation at lysine 9 (H3K9me2) and increased the euchromatic histone methyltransferases EHMT1 and EHMT2, which were accompanied by neuronal synaptic damage, including loss of synapses and diminished expression levels of synaptic-related proteins. Furthermore, the levels of H3K9me2 at promoters in genes that encode the synaptic-related proteins SNAP25, PSD95, Synapsin 1 and vGLUT1 were increased in primary neurons after PFF treatment, which suggests a linkage between H3K9 dimethylation and synaptic dysfunction. Inhibition of EHMT1/2 with the specific inhibitor A-366 or shRNA suppressed histone methylation and alleviated synaptic damage in primary neurons that were treated with PFFs. In addition, the synaptic damage and motor impairment in mice that were injected with PFFs were repressed by treatment with the EHMT1/2 inhibitor A-366. Thus, our findings reveal the role of histone H3 modification by EHMT1/2 in synaptic damage and motor impairment in a PFF animal model, suggesting the involvement of epigenetic dysregulation in PD pathogenesis.


Subject(s)
Motor Disorders , Parkinson Disease , Animals , Mice , Histones/metabolism , Methylation , Neurons/metabolism , alpha-Synuclein/metabolism
15.
Lancet Oncol ; 25(1): 117-125, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38092009

ABSTRACT

BACKGROUND: Golidocitinib, a selective JAK1 tyrosine-kinase inhibitor, has shown encouraging anti-tumour activity in heavily pre-treated patients with relapsed or refractory peripheral T-cell lymphoma in a phase 1 study (JACKPOT8 Part A). Here, we report the full analysis of a phase 2 study, in which we assessed the anti-tumour activity of golidocitinib in a large multinational cohort of patients. METHODS: We did a single-arm, multinational, phase 2 trial (JACKPOT8 Part B) in 49 centres in Australia, China, South Korea, and the USA. Eligible patients were adults (aged ≥18 years) with relapsed or refractory peripheral T-cell lymphoma who had received at least one previous line of systemic therapy and an Eastern Cooperative Oncology Group performance status of 0-2. Patients were given oral golidocitinib 150 mg once daily until disease progression or other discontinuation criteria were met. The primary endpoint was the CT-based objective response rate, assessed by an independent review committee (IRC) per Lugano 2014 classification. The activity analysis set included all patients who received at least one dose and whose pathological diagnosis of peripheral T-cell lymphoma had been retrospectively confirmed by a central laboratory and who had at least one measurable lesion at baseline assessed by IRC. The safety analysis set included all patients who received at least one dose of study drug. This study is registered with ClinicalTrials.gov, NCT04105010, and is closed to accrual and follow-up is ongoing. FINDINGS: Between Feb 26, 2021, and Oct 12, 2022, we assessed 161 patients for eligibility, of whom 104 (65%) were enrolled and received at least one dose of study drug; the activity analysis set included 88 (85%) patients (median age 58 years [IQR 51-67], 57 [65%] of 88 were male, 31 [35%] were female, and 83 [94%] were Asian). As of data cutoff (Aug 31, 2023; median follow-up was 13·3 months [IQR 4·9-18·4]), per IRC assessment, the objective response rate was 44·3% (95% CI 33·7-55·3; 39 of 88 patients, p<0·0001), with 21 (24%) patients having a complete response and 18 (20%) having a partial response. In the safety analysis set, 61 (59%) of 104 patients had grade 3-4 drug-related treatment-emergent adverse events. The most common grade 3-4 drug-related treatment-emergent adverse events were neutrophil count decreased (30 [29%]), white blood cell count decreased (27 [26%]), lymphocyte count decreased (22 [21%]), and platelet count decreased (21 [20%]), which were clinically manageable and reversible. 25 (24%) patients had treatment-related serious adverse events. Deaths due to treatment-emergent adverse events occurred in three (3%) patients: two (2%) due to pneumonia (one case with fungal infection [related to golidocitinib] and another one with COVID-19 infection) and one (1%) due to confusional state. INTERPRETATION: In this phase 2 study, golidocitinib showed a favourable benefit-risk profile in treating relapsed or refractory peripheral T-cell lymphoma. The results of this study warrant further randomised clinical studies to confirm activity and assess efficacy in this population. FUNDING: Dizal Pharmaceutical.


Subject(s)
Lymphoma, T-Cell, Peripheral , Adult , Humans , Male , Female , Adolescent , Middle Aged , Lymphoma, T-Cell, Peripheral/drug therapy , Retrospective Studies , Neoplasm Recurrence, Local/drug therapy , Neoplasm Recurrence, Local/pathology , Disease Progression , Janus Kinase 1/genetics , Tyrosine/therapeutic use
16.
J Biol Chem ; 299(2): 102911, 2023 02.
Article in English | MEDLINE | ID: mdl-36642187

ABSTRACT

The attachment of a sugar to a hydrophobic lipid carrier is the first step in the biosynthesis of many glycoconjugates. In the halophilic archaeon Haloarcula hispanica, HAH_1206, renamed AepG, is a predicted glycosyltransferase belonging to the CAZy Group 2 family that shares a conserved amino acid sequence with dolichol phosphate mannose synthases. In this study, the function of AepG was investigated by genetic and biochemical approaches. We found that aepG deletion led to the disappearance of dolichol phosphate-glucuronic acid. Our biochemical assays revealed that recombinant cellulose-binding, domain-tagged AepG could catalyze the formation of dolichol phosphate-glucuronic acid in time- and dose-dependent manners. Based on the in vivo and in vitro analyses, AepG was confirmed to be a dolichol phosphate glucuronosyltransferase involved in the synthesis of the acidic exopolysaccharide produced by H. hispanica. Furthermore, lack of aepG resulted in hindered growth and cell aggregation in high salt medium, indicating that AepG is vital for the adaptation of H. hispanica to a high salt environment. In conclusion, AepG is the first dolichol phosphate glucuronosyltransferase identified in any of the three domains of life and, moreover, offers a starting point for further investigation into the diverse pathways used for extracellular polysaccharide biosynthesis in archaea.


Subject(s)
Haloarcula , Amino Acid Sequence , Dolichol Phosphates/metabolism , Haloarcula/metabolism , Transferases/metabolism , Polysaccharides/metabolism
17.
J Am Chem Soc ; 146(9): 6307-6316, 2024 Mar 06.
Article in English | MEDLINE | ID: mdl-38381876

ABSTRACT

Saturated hydrocarbon bonds are ubiquitous in organic molecules; to date, the selective functionalization of C(sp3)-H bonds continues to pose a notorious difficulty, thereby garnering significant attention from the synthetic chemistry community. During the past several decades, a wide array of powerful new methodologies has been developed to enantioselectively modify C(sp3)-H bonds that is successfully applied in asymmetric formation of diverse bonds, including C-C, C-N, and C-O bonds; nevertheless, the asymmetric C(sp3)-H alkylation is elusive and, therefore, far less explored. In this work, we report a direct and robust strategy to construct highly valuable enantioenriched unnatural α-amino acid (α-AA) cognates and peptides by a copper-catalyzed enantioselective remote C(sp3)-H alkylation of N-fluorocarboxamides and readily accessible glycine esters under ambient conditions. The key to success lies in the optically active Cu catalyst generated through the coordination of glycine derivatives to enantiopure bisphosphine/Cu(I) species, which is beneficial to the single electronic reduction of N-fluorocarboxamides and the subsequent stereodetermining alkylation. More importantly, all types (primary, secondary, tertiary, and even α-oxy) of δ-C(sp3)-H bonds could be site- and stereospecifically activated by the kinetically favored 1,5-hydrogen atom transfer (1,5-HAT) step.


Subject(s)
Copper , Glycine , Copper/chemistry , Alkylation , Peptides/chemistry , Catalysis
18.
Antimicrob Agents Chemother ; 68(5): e0011824, 2024 May 02.
Article in English | MEDLINE | ID: mdl-38526048

ABSTRACT

Quorum sensing is a type of cell-cell communication that modulates various biological activities of bacteria. Previous studies indicate that quorum sensing contributes to the evolution of bacterial resistance to antibiotics, but the underlying mechanisms are not fully understood. In this study, we grew Pseudomonas aeruginosa in the presence of sub-lethal concentrations of ciprofloxacin, resulting in a large increase in ciprofloxacin minimal inhibitory concentration. We discovered that quorum sensing-mediated phenazine biosynthesis was significantly enhanced in the resistant isolates, where the quinolone circuit was the predominant contributor to this phenomenon. We found that production of pyocyanin changed carbon flux and showed that the effect can be partially inhibited by the addition of pyruvate to cultures. This study illustrates the role of quorum sensing-mediated phenotypic resistance and suggests a strategy for its prevention.


Subject(s)
Anti-Bacterial Agents , Ciprofloxacin , Drug Resistance, Bacterial , Microbial Sensitivity Tests , Phenazines , Pseudomonas aeruginosa , Pyocyanine , Quorum Sensing , Pseudomonas aeruginosa/drug effects , Pseudomonas aeruginosa/genetics , Ciprofloxacin/pharmacology , Quorum Sensing/drug effects , Phenazines/pharmacology , Phenazines/metabolism , Anti-Bacterial Agents/pharmacology , Pyocyanine/biosynthesis , Drug Resistance, Bacterial/genetics , Gene Expression Regulation, Bacterial/drug effects , Quinolones/pharmacology
19.
BMC Plant Biol ; 24(1): 113, 2024 Feb 16.
Article in English | MEDLINE | ID: mdl-38365619

ABSTRACT

BACKGROUND: The WRKY gene family is one of the largest families of transcription factors in higher plants, and WRKY transcription factors play important roles in plant growth and development as well as in response to abiotic stresses; however, the WRKY gene family in pea has not been systematically reported. RESULTS: In this study, 89 pea WRKY genes were identified and named according to the random distribution of PsWRKY genes on seven chromosomes. The gene family was found to have nine pairs of tandem duplicates and 19 pairs of segment duplicates. Phylogenetic analyses of the PsWRKY and 60 Arabidopsis WRKY proteins were performed to determine their homology, and the PsWRKYs were classified into seven subfamilies. Analysis of the physicochemical properties, motif composition, and gene structure of pea WRKYs revealed significant differences in the physicochemical properties within the PsWRKY family; however, their gene structure and protein-conserved motifs were highly conserved among the subfamilies. To further investigate the evolutionary relationships of the PsWRKY family, we constructed comparative syntenic maps of pea with representative monocotyledonous and dicotyledonous plants and found that it was most recently homologous to the dicotyledonous WRKY gene families. Cis-acting element analysis of PsWRKY genes revealed that this gene family can respond to hormones, such as abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellin (GA), methyl jasmonate (MeJA), and salicylic acid (SA). Further analysis of the expression of 14 PsWRKY genes from different subfamilies in different tissues and fruit developmental stages, as well as under five different hormone treatments, revealed differences in their expression patterns in the different tissues and fruit developmental stages, as well as under hormone treatments, suggesting that PsWRKY genes may have different physiological functions and respond to hormones. CONCLUSIONS: In this study, we systematically identified WRKY genes in pea for the first time and further investigated their physicochemical properties, evolution, and expression patterns, providing a theoretical basis for future studies on the functional characterization of pea WRKY genes during plant growth and development.


Subject(s)
Genes, Plant , Transcription Factors , Transcription Factors/genetics , Transcription Factors/metabolism , Pisum sativum/genetics , Phylogeny , Multigene Family , Gene Expression Regulation, Plant , Gene Expression Profiling , Hormones , Plant Proteins/metabolism , Stress, Physiological/genetics
20.
Am J Gastroenterol ; 2024 Apr 18.
Article in English | MEDLINE | ID: mdl-38477473

ABSTRACT

INTRODUCTION: Although cytologic examination of biliary stricture brushings obtained by endoscopic retrograde cholangiopancreatography is commonly used for diagnosing malignant biliary strictures (MBSs), it has low sensitivity. Several new brushes have capabilities that are still being debated. We have developed a novel brush working from conventional back-and-forth movement to rotation in situ (RIS) that may be more efficient for MBS sampling. We aimed to compare the MBS detection sensitivity of our RIS brush with that of the conventional brush. METHODS: In this multicenter prospective study, we enrolled patients who underwent endoscopic retrograde cholangiopancreatography for suspected MBSs involving biliary stricture brushings obtained using our RIS brush. The historical control group consisted of the 30-brushing arm of our previous randomized trial (patient inclusion, 2018-2020) that used the study design in the same centers and with the same endoscopists as were used in this study. The primary outcome was to compare the sensitivity and specificity of detecting MBSs by cytologic evaluation of biliary stricture brushings between the 2 groups. RESULTS: We enrolled 155 patients in the intent-to-treat analysis. Using the same number of brushing cycles, the RIS brush showed a higher sensitivity than the conventional brush (0.73 vs 0.56, P = 0.003). In per-protocol population, the sensitivity was also higher in the RIS brush group than in the conventional brush group (0.75 vs 0.57, P = 0.002). Multivariate analysis revealed that the RIS brush was the only predictive factor for MBS detection. No significant differences were observed in procedure-related complications between the 2 groups. DISCUSSION: The RIS brush was a promising tool for effective and safe MBS sampling and diagnosis. Further randomized studies are warranted to confirm our results (Chictr.org.cn, identifier: ChiCTR2100047270).

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