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1.
Cell ; 176(6): 1447-1460.e14, 2019 03 07.
Article in English | MEDLINE | ID: mdl-30799039

ABSTRACT

The presence of DNA in the cytoplasm is normally a sign of microbial infections and is quickly detected by cyclic GMP-AMP synthase (cGAS) to elicit anti-infection immune responses. However, chronic activation of cGAS by self-DNA leads to severe autoimmune diseases for which no effective treatment is available yet. Here we report that acetylation inhibits cGAS activation and that the enforced acetylation of cGAS by aspirin robustly suppresses self-DNA-induced autoimmunity. We find that cGAS acetylation on either Lys384, Lys394, or Lys414 contributes to keeping cGAS inactive. cGAS is deacetylated in response to DNA challenges. Importantly, we show that aspirin can directly acetylate cGAS and efficiently inhibit cGAS-mediated immune responses. Finally, we demonstrate that aspirin can effectively suppress self-DNA-induced autoimmunity in Aicardi-Goutières syndrome (AGS) patient cells and in an AGS mouse model. Thus, our study reveals that acetylation contributes to cGAS activity regulation and provides a potential therapy for treating DNA-mediated autoimmune diseases.


Subject(s)
DNA/immunology , Nucleotidyltransferases/metabolism , Self Tolerance/immunology , Acetylation , Amino Acid Sequence , Animals , Aspirin/pharmacology , Autoimmune Diseases/genetics , Autoimmune Diseases/immunology , Autoimmune Diseases/metabolism , Autoimmune Diseases of the Nervous System/genetics , Autoimmune Diseases of the Nervous System/immunology , Autoimmune Diseases of the Nervous System/metabolism , Autoimmunity , Cell Line , DNA/genetics , DNA/metabolism , Disease Models, Animal , Exodeoxyribonucleases/metabolism , HEK293 Cells , HeLa Cells , Humans , Mice , Mice, Inbred C57BL , Models, Molecular , Mutation , Nervous System Malformations/genetics , Nervous System Malformations/immunology , Nervous System Malformations/metabolism , Nucleotidyltransferases/antagonists & inhibitors , Nucleotidyltransferases/chemistry , Nucleotidyltransferases/genetics , THP-1 Cells
2.
Nat Immunol ; 20(1): 18-28, 2019 01.
Article in English | MEDLINE | ID: mdl-30510222

ABSTRACT

Cyclic GMP-AMP synthase (cGAS) is a key sensor responsible for cytosolic DNA detection. Here we report that GTPase-activating protein SH3 domain-binding protein 1 (G3BP1) is critical for DNA sensing and efficient activation of cGAS. G3BP1 enhanced DNA binding of cGAS by promoting the formation of large cGAS complexes. G3BP1 deficiency led to inefficient DNA binding by cGAS and inhibited cGAS-dependent interferon (IFN) production. The G3BP1 inhibitor epigallocatechin gallate (EGCG) disrupted existing G3BP1-cGAS complexes and inhibited DNA-triggered cGAS activation, thereby blocking DNA-induced IFN production both in vivo and in vitro. EGCG administration blunted self DNA-induced autoinflammatory responses in an Aicardi-Goutières syndrome (AGS) mouse model and reduced IFN-stimulated gene expression in cells from a patient with AGS. Thus, our study reveals that G3BP1 physically interacts with and primes cGAS for efficient activation. Furthermore, EGCG-mediated inhibition of G3BP1 provides a potential treatment for cGAS-related autoimmune diseases.


Subject(s)
Autoimmune Diseases of the Nervous System/metabolism , DNA Helicases/metabolism , Multiprotein Complexes/metabolism , Nervous System Malformations/metabolism , Nucleotidyltransferases/metabolism , Poly-ADP-Ribose Binding Proteins/metabolism , RNA Helicases/metabolism , RNA Recognition Motif Proteins/metabolism , Animals , Autoantigens/immunology , Autoantigens/metabolism , Autoimmune Diseases of the Nervous System/drug therapy , Autoimmune Diseases of the Nervous System/genetics , Catechin/analogs & derivatives , Catechin/therapeutic use , Clustered Regularly Interspaced Short Palindromic Repeats , Cytosol/immunology , Cytosol/metabolism , DNA/immunology , DNA/metabolism , DNA Helicases/antagonists & inhibitors , DNA Helicases/genetics , Disease Models, Animal , Exodeoxyribonucleases/genetics , HEK293 Cells , HeLa Cells , Humans , Interferons/metabolism , Mice , Mice, Knockout , Nervous System Malformations/drug therapy , Nervous System Malformations/genetics , Neuroprotective Agents/therapeutic use , Phosphoproteins/genetics , Poly-ADP-Ribose Binding Proteins/antagonists & inhibitors , Poly-ADP-Ribose Binding Proteins/genetics , Protein Binding , RNA Helicases/antagonists & inhibitors , RNA Helicases/genetics , RNA Recognition Motif Proteins/antagonists & inhibitors , RNA Recognition Motif Proteins/genetics
3.
Proc Natl Acad Sci U S A ; 121(37): e2409201121, 2024 Sep 10.
Article in English | MEDLINE | ID: mdl-39240973

ABSTRACT

Transition metal oxides ion diffusion channels have been developed for ammonium-ion batteries (AIBs). However, the influence of microstructural features of diffusion channels on the storage and diffusion behavior of NH4+ is not fully unveiled. In this study, by using MnCo2O4 spinel as a model electrode, the asymmetric ion diffusion channels of MnCo2O4 have been regulated through bond length optimization strategy and investigate the effect of channel size on the diffusion process of NH4+. In addition, the reducing channel size significantly decreases NH4+ adsorption energy, thereby accelerating hydrogen bond formation/fracture kinetics and NH4+ reversible diffusion within 3D asymmetric channels. The optimized MnCo2O4 with oxygen vacancies/carbon nanotubes composite exhibits impressive specific capacity (219.2 mAh g-1 at 0.1 A g-1) and long-cycle stability. The full cell with 3,4,9,10-perylenetetracarboxylic diimide anode demonstrates a remarkable energy density of 52.3 Wh kg-1 and maintains 91.9% capacity after 500 cycles. This finding provides a unique approach for the development of cathode materials in AIBs.

4.
Proc Natl Acad Sci U S A ; 121(6): e2318174121, 2024 Feb 06.
Article in English | MEDLINE | ID: mdl-38289955

ABSTRACT

Atomically dispersed catalysts are a promising alternative to platinum group metal catalysts for catalyzing the oxygen reduction reaction (ORR), while limited durability during the electrocatalytic process severely restricts their practical application. Here, we report an atomically dispersed Co-doped carbon-nitrogen bilayer catalyst with unique dual-axial Co-C bonds (denoted as Co/DACN) by a smart phenyl-carbon-induced strategy, realizing highly efficient electrocatalytic ORR in both alkaline and acidic media. The corresponding half-wave potential for ORR is up to 0.85 and 0.77 V (vs. reversible hydrogen electrode (RHE)) in 0.5 M H2SO4 and 0.1 M KOH, respectively, representing the best ORR activity among all non-noble metal catalysts reported to date. Impressively, the Zn-air battery (ZAB) equipped with Co/DACN cathode achieves outstanding durability after 1,688 h operation at 10 mA cm-2 with a high current density (154.2 mA cm-2) and a peak power density (210.1 mW cm-2). Density functional theory calculations reveal that the unique dual-axial cross-linking Co-C bonds of Co/DACN significantly enhance the stability during ORR and also facilitate the 4e- ORR pathway by forming a joint electron pool due to the improved interlayer electron mobility. We believe that axial engineering opens a broad avenue to develop high-performance heterogeneous electrocatalysts for advanced energy conversion and storage.

5.
Proc Natl Acad Sci U S A ; 121(4): e2312556121, 2024 Jan 23.
Article in English | MEDLINE | ID: mdl-38227655

ABSTRACT

Hemorrhagic fever with renal syndrome (HFRS) is a zoonotic disease caused by the rodent-transmitted orthohantaviruses (HVs), with China possessing the most cases globally. The virus hosts in China are Apodemus agrarius and Rattus norvegicus, and the disease spread is strongly influenced by global climate dynamics. To assess and predict the spatiotemporal trends of HFRS from 2005 to 2098, we collected historical HFRS data in mainland China (2005-2020), historical and projected climate and population data (2005-2098), and spatial variables including biotic, environmental, topographical, and socioeconomic. Spatiotemporal predictions and mapping were conducted under 27 scenarios incorporating multiple integrated representative concentration pathway models and population scenarios. We identify the type of magistral HVs host species as the best spatial division, including four region categories. Seven extreme climate indices associated with temperature and precipitation have been pinpointed as key factors affecting the trends of HFRS. Our predictions indicate that annual HFRS cases will increase significantly in 62 of 356 cities in mainland China. Rattus regions are predicted to be the most active, surpassing Apodemus and Mixed regions. Eighty cities are identified as at severe risk level for HFRS, each with over 50 reported cases annually, including 22 new cities primarily located in East China and Rattus regions after 2020, while 6 others develop new risk. Our results suggest that the risk of HFRS will remain high through the end of this century, with Rattus norvegicus being the most active host, and that extreme climate indices are significant risk factors. Our findings can inform evidence-based policymaking regarding future risk of HFRS.


Subject(s)
Hemorrhagic Fever with Renal Syndrome , Rats , Animals , Hemorrhagic Fever with Renal Syndrome/epidemiology , Hemorrhagic Fever with Renal Syndrome/etiology , Climate , Zoonoses , China/epidemiology , Murinae , Incidence
6.
Plant Cell ; 35(6): 2114-2131, 2023 05 29.
Article in English | MEDLINE | ID: mdl-36861340

ABSTRACT

Brassinosteroid (BR), a growth-promoting phytohormone, regulates many plant growth processes including cell development. However, the mechanism by which BR regulates fiber growth is poorly understood. Cotton (Gossypium hirsutum) fibers are an ideal single-cell model in which to study cell elongation due to their length. Here we report that BR controls cotton fiber elongation by modulating very-long-chain fatty acid (VLCFA) biosynthesis. BR deficiency reduces the expression of 3-ketoacyl-CoA synthases (GhKCSs), the rate-limiting enzymes involved in VLCFA biosynthesis, leading to lower saturated VLCFA contents in pagoda1 (pag1) mutant fibers. In vitro ovule culture experiments show that BR acts upstream of VLCFAs. Silencing of BRI1-EMS-SUPPRESOR 1.4 (GhBES1.4), encoding a master transcription factor of the BR signaling pathway, significantly reduces fiber length, whereas GhBES1.4 overexpression produces longer fibers. GhBES1.4 regulates endogenous VLCFA contents and directly binds to BR RESPONSE ELEMENTS (BRREs) in the GhKCS10_At promoter region, which in turn regulates GhKCS10_At expression to increase endogenous VLCFA contents. GhKCS10_At overexpression promotes cotton fiber elongation, whereas GhKCS10_At silencing inhibits cotton fiber growth, supporting a positive regulatory role for GhKCS10_At in fiber elongation. Overall, these results uncover a mechanism of fiber elongation through crosstalk between BR and VLCFAs at the single-cell level.


Subject(s)
Brassinosteroids , Cotton Fiber , Gossypium/genetics , Cell Differentiation , Fatty Acids
7.
Plant J ; 117(2): 464-482, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37872890

ABSTRACT

Rhodiola L. is a genus that has undergone rapid radiation in the mid-Miocene and may represent a typic case of adaptive radiation. Many species of Rhodiola have also been widely used as an important adaptogen in traditional medicines for centuries. However, a lack of high-quality chromosome-level genomes hinders in-depth study of its evolution and biosynthetic pathway of secondary metabolites. Here, we assembled two chromosome-level genomes for two Rhodiola species with different chromosome number and sexual system. The assembled genome size of R. chrysanthemifolia (2n = 14; hermaphrodite) and R. kirilowii (2n = 22; dioecious) were of 402.67 and 653.62 Mb, respectively, with approximately 57.60% and 69.22% of transposable elements (TEs). The size difference between the two genomes was mostly due to proliferation of long terminal repeat-retrotransposons (LTR-RTs) in the R. kirilowii genome. Comparative genomic analysis revealed possible gene families responsible for high-altitude adaptation of Rhodiola, including a homolog of plant cysteine oxidase 2 gene of Arabidopsis thaliana (AtPCO2), which is part of the core molecular reaction to hypoxia and contributes to the stability of Group VII ethylene response factors (ERF-VII). We found extensive chromosome fusion/fission events and structural variations between the two genomes, which might have facilitated the initial rapid radiation of Rhodiola. We also identified candidate genes in the biosynthetic pathway of salidroside. Overall, our results provide important insights into genome evolution in plant rapid radiations, and possible roles of chromosome fusion/fission and structure variation played in rapid speciation.


Subject(s)
Glucosides , Phenols , Rhodiola , Rhodiola/genetics , Rhodiola/metabolism , Biosynthetic Pathways , Genome Size , Chromosomes , Evolution, Molecular
8.
Plant J ; 120(2): 491-504, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39172024

ABSTRACT

Cotton fiber (Gossypium hirsutum) serves as an ideal model for investigating the molecular mechanisms of plant cell elongation at the single-cell level. Brassinosteroids (BRs) play a crucial role in regulating plant growth and development. However, the mechanism by which BR influences cotton fiber elongation remains incompletely understood. In this study, we identified EXORDIUM-like (GhEXL3) through transcriptome analysis of fibers from BR-deficient cotton mutant pagoda 1 (pag1) and BRI1-EMS-SUPPRESSOR 1 (GhBES1.4, encoding a central transcription factor of BR signaling) overexpression cotton lines. Knockout of GhEXL3 using CRISPR/Cas9 was found to impede cotton fiber elongation, while its overexpression promoted fiber elongation, suggesting a positive regulatory function for GhEXL3 in fiber elongation. Furthermore, in vitro ovule culture experiments revealed that the overexpression of GhEXL3 partially counteracted the inhibitory effects of brassinazole (BRZ) on cotton fiber elongation, providing additional evidence of GhEXL3 involvement in BR signaling pathways. Moreover, our findings demonstrate that GhBES1.4 directly binds to the E-box (CACGTG) motif in the GhEXL3 promoter region and enhances its transcription. RNA-seq analysis revealed that overexpression of GhEXL3 upregulated the expression of EXPs, XTHs, and other genes associated with fiber cell elongation. Overall, our study contributes to understanding the mechanism by which BR regulates the elongation of cotton fibers through the direct modulation of GhEXL3 expression by GhBES1.4.


Subject(s)
Brassinosteroids , Cotton Fiber , Gene Expression Regulation, Plant , Gossypium , Plant Proteins , Gossypium/genetics , Gossypium/metabolism , Brassinosteroids/metabolism , Plant Proteins/metabolism , Plant Proteins/genetics , Transcription Factors/metabolism , Transcription Factors/genetics , Plants, Genetically Modified , Plant Growth Regulators/metabolism , Signal Transduction
9.
Brief Bioinform ; 24(2)2023 03 19.
Article in English | MEDLINE | ID: mdl-36681902

ABSTRACT

Identification of potential targets for known bioactive compounds and novel synthetic analogs is of considerable significance. In silico target fishing (TF) has become an alternative strategy because of the expensive and laborious wet-lab experiments, explosive growth of bioactivity data and rapid development of high-throughput technologies. However, these TF methods are based on different algorithms, molecular representations and training datasets, which may lead to different results when predicting the same query molecules. This can be confusing for practitioners in practical applications. Therefore, this study systematically evaluated nine popular ligand-based TF methods based on target and ligand-target pair statistical strategies, which will help practitioners make choices among multiple TF methods. The evaluation results showed that SwissTargetPrediction was the best method to produce the most reliable predictions while enriching more targets. High-recall similarity ensemble approach (SEA) was able to find real targets for more compounds compared with other TF methods. Therefore, SwissTargetPrediction and SEA can be considered as primary selection methods in future studies. In addition, the results showed that k = 5 was the optimal number of experimental candidate targets. Finally, a novel ensemble TF method based on consensus voting is proposed to improve the prediction performance. The precision of the ensemble TF method outperforms the individual TF method, indicating that the ensemble TF method can more effectively identify real targets within a given top-k threshold. The results of this study can be used as a reference to guide practitioners in selecting the most effective methods in computational drug discovery.


Subject(s)
Algorithms , Ligands
10.
Brief Bioinform ; 24(1)2023 01 19.
Article in English | MEDLINE | ID: mdl-36642412

ABSTRACT

Machine learning-based scoring functions (MLSFs) have become a very favorable alternative to classical scoring functions because of their potential superior screening performance. However, the information of negative data used to construct MLSFs was rarely reported in the literature, and meanwhile the putative inactive molecules recorded in existing databases usually have obvious bias from active molecules. Here we proposed an easy-to-use method named AMLSF that combines active learning using negative molecular selection strategies with MLSF, which can iteratively improve the quality of inactive sets and thus reduce the false positive rate of virtual screening. We chose energy auxiliary terms learning as the MLSF and validated our method on eight targets in the diverse subset of DUD-E. For each target, we screened the IterBioScreen database by AMLSF and compared the screening results with those of the four control models. The results illustrate that the number of active molecules in the top 1000 molecules identified by AMLSF was significantly higher than those identified by the control models. In addition, the free energy calculation results for the top 10 molecules screened out by the AMLSF, null model and control models based on DUD-E also proved that more active molecules can be identified, and the false positive rate can be reduced by AMLSF.


Subject(s)
Proteins , Proteins/metabolism , Databases, Factual , Ligands , Molecular Docking Simulation , Protein Binding
11.
Nature ; 568(7752): 336-343, 2019 04.
Article in English | MEDLINE | ID: mdl-30996318

ABSTRACT

The brains of humans and other mammals are highly vulnerable to interruptions in blood flow and decreases in oxygen levels. Here we describe the restoration and maintenance of microcirculation and molecular and cellular functions of the intact pig brain under ex vivo normothermic conditions up to four hours post-mortem. We have developed an extracorporeal pulsatile-perfusion system and a haemoglobin-based, acellular, non-coagulative, echogenic, and cytoprotective perfusate that promotes recovery from anoxia, reduces reperfusion injury, prevents oedema, and metabolically supports the energy requirements of the brain. With this system, we observed preservation of cytoarchitecture; attenuation of cell death; and restoration of vascular dilatory and glial inflammatory responses, spontaneous synaptic activity, and active cerebral metabolism in the absence of global electrocorticographic activity. These findings demonstrate that under appropriate conditions the isolated, intact large mammalian brain possesses an underappreciated capacity for restoration of microcirculation and molecular and cellular activity after a prolonged post-mortem interval.


Subject(s)
Autopsy , Brain/blood supply , Brain/cytology , Cerebrovascular Circulation , Microcirculation , Swine , Animals , Brain/metabolism , Brain/pathology , Brain Ischemia/metabolism , Brain Ischemia/pathology , Caspase 3/metabolism , Cell Survival , Cerebral Arteries/physiology , Disease Models, Animal , Hypoxia, Brain/metabolism , Hypoxia, Brain/pathology , Inflammation/metabolism , Inflammation/pathology , Neuroglia/cytology , Neurons/cytology , Neurons/metabolism , Neurons/pathology , Perfusion , Reperfusion Injury/prevention & control , Swine/blood , Synapses/metabolism , Synapses/pathology , Time Factors , Vasodilation
12.
Mol Cell ; 68(1): 185-197.e6, 2017 Oct 05.
Article in English | MEDLINE | ID: mdl-28943315

ABSTRACT

Many infections and stress signals can rapidly activate the NLRP3 inflammasome to elicit robust inflammatory responses. This activation requires a priming step, which is thought to be mainly for upregulating NLRP3 transcription. However, recent studies report that the NLRP3 inflammasome can be activated independently of transcription, suggesting that the priming process has unknown essential regulatory steps. Here, we report that JNK1-mediated NLRP3 phosphorylation at S194 is a critical priming event and is essential for NLRP3 inflammasome activation. We show that NLRP3 inflammasome activation is disrupted in NLRP3-S194A knockin mice. JNK1-mediated NLRP3 S194 phosphorylation is critical for NLRP3 deubiquitination and facilitates its self-association and the subsequent inflammasome assembly. Importantly, we demonstrate that blocking S194 phosphorylation prevents NLRP3 inflammasome activation in cryopyrin-associated periodic syndromes (CAPS). Thus, our study reveals a key priming molecular event that is a prerequisite for NLRP3 inflammasome activation. Inhibiting NLRP3 phosphorylation could be an effective treatment for NLRP3-related diseases.


Subject(s)
Inflammasomes/genetics , Macrophages/immunology , Mitogen-Activated Protein Kinase 8/genetics , NLR Family, Pyrin Domain-Containing 3 Protein/genetics , Shock, Septic/genetics , Amino Acid Sequence , Animals , Deubiquitinating Enzymes/genetics , Deubiquitinating Enzymes/immunology , Escherichia coli/chemistry , Female , Gene Expression Regulation , HEK293 Cells , Humans , Inflammasomes/immunology , Lipopolysaccharides/pharmacology , Macrophages/pathology , Male , Mice , Mice, Transgenic , Mitogen-Activated Protein Kinase 8/immunology , NLR Family, Pyrin Domain-Containing 3 Protein/deficiency , NLR Family, Pyrin Domain-Containing 3 Protein/immunology , Phosphorylation , Sequence Alignment , Sequence Homology, Amino Acid , Shock, Septic/chemically induced , Shock, Septic/mortality , Shock, Septic/pathology , Signal Transduction , Survival Analysis
13.
Nano Lett ; 24(36): 11295-11301, 2024 Sep 11.
Article in English | MEDLINE | ID: mdl-39213595

ABSTRACT

The integration of intrinsically magnetic and topologically nontrivial two-dimensional materials holds tantalizing prospects for exotic quantum anomalous Hall insulators and magnetic second-order topological insulators (SOTIs). Compared with their well-studied nonmagnetic counterparts, the pursuit of intrinsic magnetic SOTIs remains limited. In this work, we address this gap by focusing on p-d orbitals inversion, a fundamental but often overlooked phenomena in the construction of topological materials. We begin by developing a theoretical framework to elucidate p-d orbital inversion through a combined density-functional theory calculation and Wannier downfolding. Subsequently we showcase the generality of this concept in realizing ferromagnetism SOTIs by identifying two real materials with distinct lattices: 1T-VS2 monolayer in a hexagonal lattice and CrAs monolayer in a square lattice. We further compare it with other mechanisms requiring spin-orbit coupling and explore the similarities to topological Kondo insulators. Our findings establish a generic pathway toward intrinsic magnetic SOTIs.

14.
Nano Lett ; 24(5): 1687-1694, 2024 Feb 07.
Article in English | MEDLINE | ID: mdl-38253561

ABSTRACT

Revealing the in-depth structure-property relationship and designing specific capacity electrodes are particularly important for supercapacitors. Despite many efforts made to tune the composition and electronic structure of cobalt oxide for pseudocapacitance, insight into the [CoO]6 octahedron from the microstructure is still insufficient. Herein, we present a tunable [CoO]6 octahedron microstructure in LiCoO2 by a chemical delithiation process. The c-strained strain of the [CoO]6 octahedron is induced to form higher valence Co ions, and the (003) crystalline layer spacing increases to allow more rapid participation of OH- in the redox reaction. Interestingly, the specific capacity of L0.75CO2 is nearly four times higher than that of LiCoO2 at 10 mA g-1. The enhanced activity originated from the asymmetric strain [CoO]6 octahedra, resulting in enhanced electronic conductivity and Co-O hybridization for accelerated redox kinetics. This finding provides new insights into the modification strategy for pseudocapacitive transition metal oxides.

15.
Nano Lett ; 24(3): 881-889, 2024 Jan 24.
Article in English | MEDLINE | ID: mdl-38198246

ABSTRACT

Cellulose nanofiber (CNF) possesses excellent intrinsic properties, and many CNF-based high-performance structural and functional materials have been developed recently. However, the coordination of the mechanical properties and functionality is still a considerable challenge. Here, a CNF-based structural material is developed by a bioinspired gradient structure design using hollow magnetite nanoparticles and the phosphorylation-modified CNF as building blocks, which simultaneously achieves a superior mechanical performance and electromagnetic wave absorption (EMA) ability. Benefiting from the gradient design, the flexural strength of the structural material reached ∼205 MPa. Meanwhile, gradient design improves impedance matching, contributing to the high EMA ability (-59.5 dB) and wide effective absorption width (5.20 GHz). Besides, a low coefficient of thermal expansion and stable storage modulus was demonstrated as the temperature changes. The excellent mechanical, thermal, and EMA performance exhibited great potential for application in stealth equipment and electromagnetic interference protecting electronic packaging materials.

16.
BMC Bioinformatics ; 25(1): 282, 2024 Aug 28.
Article in English | MEDLINE | ID: mdl-39198740

ABSTRACT

BACKGROUND: Thermostability is a fundamental property of proteins to maintain their biological functions. Predicting protein stability changes upon mutation is important for our understanding protein structure-function relationship, and is also of great interest in protein engineering and pharmaceutical design. RESULTS: Here we present mutDDG-SSM, a deep learning-based framework that uses the geometric representations encoded in protein structure to predict the mutation-induced protein stability changes. mutDDG-SSM consists of two parts: a graph attention network-based protein structural feature extractor that is trained with a self-supervised learning scheme using large-scale high-resolution protein structures, and an eXtreme Gradient Boosting model-based stability change predictor with an advantage of alleviating overfitting problem. The performance of mutDDG-SSM was tested on several widely-used independent datasets. Then, myoglobin and p53 were used as case studies to illustrate the effectiveness of the model in predicting protein stability changes upon mutations. Our results show that mutDDG-SSM achieved high performance in estimating the effects of mutations on protein stability. In addition, mutDDG-SSM exhibited good unbiasedness, where the prediction accuracy on the inverse mutations is as well as that on the direct mutations. CONCLUSION: Meaningful features can be extracted from our pre-trained model to build downstream tasks and our model may serve as a valuable tool for protein engineering and drug design.


Subject(s)
Mutation , Protein Stability , Proteins , Proteins/chemistry , Proteins/genetics , Proteins/metabolism , Myoglobin/chemistry , Myoglobin/genetics , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/chemistry , Tumor Suppressor Protein p53/metabolism , Computational Biology/methods , Deep Learning , Supervised Machine Learning , Databases, Protein , Protein Conformation
17.
J Biol Chem ; 299(5): 104592, 2023 05.
Article in English | MEDLINE | ID: mdl-36894019

ABSTRACT

Human DDX5 and its yeast ortholog Dbp2 are ATP-dependent RNA helicases that play a key role in normal cell processes, cancer development, and viral infection. The crystal structure of the RecA1-like domain of DDX5 is available but the global structure of DDX5/Dbp2 subfamily proteins remains to be elucidated. Here, we report the first X-ray crystal structures of the Dbp2 helicase core alone and in complex with ADP at 3.22 Å and 3.05 Å resolutions, respectively. The structures of the ADP-bound post-hydrolysis state and apo-state demonstrate the conformational changes that occur when the nucleotides are released. Our results showed that the helicase core of Dbp2 shifted between open and closed conformation in solution but the unwinding activity was hindered when the helicase core was restricted to a single conformation. A small-angle X-ray scattering experiment showed that the disordered amino (N) tail and carboxy (C) tails are flexible in solution. Truncation mutations confirmed that the terminal tails were critical for the nucleic acid binding, ATPase, and unwinding activities, with the C-tail being exclusively responsible for the annealing activity. Furthermore, we labeled the terminal tails to observe the conformational changes between the disordered tails and the helicase core upon binding nucleic acid substrates. Specifically, we found that the nonstructural terminal tails bind to RNA substrates and tether them to the helicase core domain, thereby conferring full helicase activities to the Dbp2 protein. This distinct structural characteristic provides new insight into the mechanism of DEAD-box RNA helicases.


Subject(s)
DEAD-box RNA Helicases , Saccharomyces cerevisiae Proteins , Humans , DEAD-box RNA Helicases/metabolism , RNA/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Molecular Conformation , DNA Helicases/metabolism
18.
Plant J ; 115(6): 1729-1745, 2023 09.
Article in English | MEDLINE | ID: mdl-37326240

ABSTRACT

The steroidal hormone brassinosteroid (BR) has been shown to positively regulate cell expansion in plants. However, the specific mechanism by which BR controls this process has not been fully understood. In this study, RNA-seq and DAP-seq analysis of GhBES1.4 (a core transcription factor in BR signaling) were used to identify a cotton cell cycle-dependent kinase inhibitor called GhKRP6. The study found that GhKRP6 was significantly induced by the BR hormone and that GhBES1.4 directly promoted the expression of GhKRP6 by binding to the CACGTG motif in its promoter region. GhKRP6-silenced cotton plants had smaller leaves with more cells and reduced cell size. Furthermore, endoreduplication was inhibited, which affected cell expansion and ultimately decreased fiber length and seed size in GhKRP6-silenced plants compared with the control. The KEGG enrichment results of control and VIGS-GhKRP6 plants revealed differential expression of genes related to cell wall biosynthesis, MAPK, and plant hormone transduction pathways - all of which are related to cell expansion. Additionally, some cyclin-dependent kinase (CDK) genes were upregulated in the plants with silenced GhKRP6. Our study also found that GhKRP6 could interact directly with a cell cycle-dependent kinase called GhCDKG. Taken together, these results suggest that BR signaling influences cell expansion by directly modulating the expression of cell cycle-dependent kinase inhibitor GhKRP6 via GhBES1.4.


Subject(s)
Brassinosteroids , Gossypium , Brassinosteroids/pharmacology , Brassinosteroids/metabolism , Gossypium/genetics , Gossypium/metabolism , Cell Cycle/genetics , Plants/metabolism , Hormones , Gene Expression Regulation, Plant , Plant Proteins/genetics , Plant Proteins/metabolism
19.
Plant J ; 115(4): 967-985, 2023 08.
Article in English | MEDLINE | ID: mdl-37158663

ABSTRACT

N6 -Methyladenosine (m6 A) is the most abundant methylation modification in eukaryotic mRNA. The discovery of the dynamic and reversible regulatory mechanism of m6 A has greatly promoted the development of m6 A-led epitranscriptomics. However, the characterization of m6 A in cotton fiber is still unknown. Here, we reveal the potential link between m6 A modification and cotton fiber elongation by parallel m6 A-immunoprecipitation-sequencing (m6 A-seq) and RNA-seq analysis of fibers from the short fiber mutants Ligonliness-2 (Li2 ) and wild-type (WT). This study demonstrated a higher level of m6 A in the Li2 mutant, with the enrichment of m6 A modifications in the stop codon, 3'-untranslated region and coding sequence regions than in WT cotton. In the correlation analysis between genes containing differential m6 A modifications and differentially expressed genes, we identified several genes that could potentially regulate fiber elongation, including cytoskeleton, microtubule binding, cell wall and transcription factors (TFs). We further confirmed that the methylation of m6 A affected the mRNA stability of these fiber elongation-related genes including the TF GhMYB44, which showed the highest expression level in the RNA-seq data and m6 A methylation in the m6 A-seq data. Next, the overexpression of GhMYB44 reduces fiber elongation, whereas the silencing of GhMYB44 produces longer fibers. In summary, these results uncover that m6 A methylation regulated the expression of genes related to fiber development by affecting mRNA's stability, ultimately affecting cotton fiber elongation.


Subject(s)
Cotton Fiber , Gossypium , RNA-Seq , RNA, Messenger/genetics , RNA, Messenger/metabolism , Gossypium/genetics , Gossypium/metabolism , Gene Expression Regulation, Plant/genetics
20.
J Am Chem Soc ; 2024 Oct 31.
Article in English | MEDLINE | ID: mdl-39480136

ABSTRACT

Electrosynthesis has emerged as a versatile and sustainable tool in organic chemistry, offering an efficient pathway for the construction of complex molecular architectures under mild and environmentally benign conditions. Traditional electrochemical approaches, however, predominantly rely on either anodic oxidation or cathodic reduction, limiting their capacity to achieve redox-neutral transformations using a single electrode. In this work, we introduce a linear paired electrolysis strategy that circumvents these limitations, enabling a redox-neutral (3 + 2) annulation of benzofuran with vinyldiazo compounds. This method facilitates the formation of benzofuran-fused tricyclic scaffolds, which are valuable in synthetic chemistry and medicinal applications. The transformation proceeds through sequential anodic oxidation and cathodic reduction, leveraging a radical cation pathway to deliver polycyclic compounds with high selectivity. The efficiency and mechanism of this process are thoroughly validated using cyclic voltammetry and in situ electrochemical mass spectrometry (EC-MS) and supported by theoretical calculations, shedding light on the potential of redox-neutral electrochemical transformations.

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