Peng C

References (29)

Title : Quantitative proteomic analysis reveals the mechanism and key esterase of beta-cypermethrin degradation in a bacterial strain from fermented food - Peng_2024_Pestic.Biochem.Physiol_201_105858
Author(s) : Peng C , Tang J , Zhou X , Zhou H , Zhang Y , Wang S , Wang W , Xiang W , Zhang Q , Yu X , Cai T
Ref : Pestic Biochem Physiol , 201 :105858 , 2024
Abstract : Beta-cypermethrin (beta-CY) residues in food are an important threat to human health. Microorganisms can degrade beta-CY residues during fermentation of fruits and vegetables, while the mechanism is not clear. In this study, a comprehensively investigate of the degradation mechanism of beta-CY in a food microorganism was conducted based on proteomics analysis. The beta-CY degradation bacteria Gordonia alkanivorans GH-1 was derived from fermented Pixian Doubanjiang. Its crude enzyme extract could degrade 77.11% of beta-CY at a concentration of 45 mg/L within 24 h. Proteomics analysis revealed that the ester bond of beta-CY is broken under the action of esterase to produce 3-phenoxy benzoic acid, which was further degraded by oxidoreductase and aromatic degrading enzyme. The up-regulation expression of oxidoreductase and esterase was confirmed by transcriptome and quantitative reverse transcription PCR. Meanwhile, the expression of esterase Est280 in Escherichia coli BL21 (DE3) resulted in a 48.43% enhancement in the degradation efficiency of beta-CY, which confirmed that this enzyme was the key enzyme in the process of beta-CY degradation. This study reveals the degradation mechanism of beta-CY by microorganisms during food fermentation, providing a theoretical basis for the application of food microorganisms in beta-CY residues.
ESTHER : Peng_2024_Pestic.Biochem.Physiol_201_105858
PubMedSearch : Peng_2024_Pestic.Biochem.Physiol_201_105858
PubMedID: 38685237

Title : Resolution of N-acetyl-DL-methionine methyl ester by the lipase from Brucella thiophenivorans - Li_2024_Chirality_36_e23643
Author(s) : Li X , Li Q , Yang L , Huang L , Peng C , Zheng J
Ref : Chirality , 36 :e23643 , 2024
Abstract : In this study, lipase-catalyzed resolution of N-acetyl-DL-methionine methyl ester (N-Ac-DL-MetOMe) was evaluated. A lipase from Brucella thiophenivorans was prone to exhibit high activity and excellent enantioselectivity toward N-Ac-DL-MetOMe to produce the key chiral intermediate N-acetyl-L-methionine methyl ester (N-Ac-L-MetOMe). The results showed that the enzymatic reaction was carried out in 100 g/L racemic substrate for 2 h, the conversion reached 51.3%, the enantiomeric excess value N-Ac-L-MetOMe exceeded 99%, and the enantiomeric ratio value >200. Therefore, the lipase from B. thiophenivorans has potential prospects for the resolution of N-Ac-DL-MetOMe to produce the important intermediate N-Ac-L-MetOMe.
ESTHER : Li_2024_Chirality_36_e23643
PubMedSearch : Li_2024_Chirality_36_e23643
PubMedID: 38384156

Title : An overview of microbial enzymatic approaches for pectin degradation - Li_2023_Int.J.Biol.Macromol_254_127804
Author(s) : Li J , Peng C , Mao A , Zhong M , Hu Z
Ref : Int J Biol Macromol , 254 :127804 , 2023
Abstract : Pectin, a complex natural macromolecule present in primary cell walls, exhibits high structural diversity. Pectin is composed of a main chain, which contains a high amount of partly methyl-esterified galacturonic acid (GalA), and numerous types of side chains that contain almost 17 different monosaccharides and over 20 different linkages. Due to this peculiar structure, pectin exhibits special physicochemical properties and a variety of bioactivities. For example, pectin exhibits strong bioactivity only in a low molecular weight range. Many different degrading enzymes, including hydrolases, lyases and esterases, are needed to depolymerize pectin due to its structural complexity. Pectin degradation involves polygalacturonases/rhamnogalacturonases and pectate/pectin lyases, which attack the linkages in the backbone via hydrolytic and beta-elimination modes, respectively. Pectin methyl/acetyl esterases involved in the de-esterification of pectin also play crucial roles. Many alpha-L-rhamnohydrolases, unsaturated rhamnogalacturonyl hydrolases, arabinanases and galactanases also contribute to heterogeneous pectin degradation. Although numerous microbial pectin-degrading enzymes have been described, the mechanisms involved in the coordinated degradation of pectin through these enzymes remain unclear. In recent years, the degradation of pectin by Bacteroides has received increasing attention, as Bacteroides species contain a unique genetic structure, polysaccharide utilization loci (PULs). The specific PULs of pectin degradation in Bacteroides species are a new field to study pectin metabolism in gut microbiota. This paper reviews the scientific information available on pectin structural characteristics, pectin-degrading enzymes, and PULs for the specific degradation of pectin.
ESTHER : Li_2023_Int.J.Biol.Macromol_254_127804
PubMedSearch : Li_2023_Int.J.Biol.Macromol_254_127804
PubMedID: 37913880

Title : Polylactic acid microplastics induce higher biotoxicity of decabromodiphenyl ethane on earthworms (Eisenia fetida) compared to polyethylene and polypropylene microplastics - Han_2022_Sci.Total.Environ__160909
Author(s) : Han Y , Fu M , Wu J , Zhou S , Qiao Z , Peng C , Zhang W , Liu F , Ye C , Yang J
Ref : Sci Total Environ , :160909 , 2022
Abstract : Decabromodiphenyl ethane (DBDPE) and microplastics (MPs), such as fossil-based polymers polyethylene (PE), polypropylene (PP), and bio-based plastics polylactic acid (PLA) are abundant in e-waste dismantling areas. However, the information on the effects of DBDPE combined with MPs (DBDPE-MPs) on earthworms is still limited. In this study, we explored the impacts of DBDPE-MPs on neurotoxic biomarkers, tissue damage, and transcriptomics of Eisenia fetida by simulating different exposure patterns of 10 mg kg(-1) DBDPE and 10 mg kg(-1) DBDPE-MPs (PLA, PP, and PE). Results showed that the activities of acetylcholinesterase, Na(+)/K(+)-ATPase, Ca(2+)/Mg(2+)-ATPase, carboxylate enzyme, and the contents of calcium and glutamate were significantly stimulated. DBDPE-MP co-exposure caused more severe damage to the epidermis, muscles, and tissues. Transcriptomic analysis revealed that differentially expressed genes (DEGs) of DBDPE-MPs were mainly related to inflammation, the immune system, digestive system, endocrine system, and metabolism. DBDPE and PP-MPs had similar influences on immunity and metabolism. However, DBDPE-PLA and DBDPE-PE further affected the endocrine system and signaling pathways. Specific DEGs showed that detoxification systems in the case of MPs were significantly upregulated. The study indicated that MPs exacerbated DBDPE toxicity in the nervous system, epidermis, and gene regulation of E. fetida, helping to assess the ecological risks of e-wastes and microplastics in soil.
ESTHER : Han_2022_Sci.Total.Environ__160909
PubMedSearch : Han_2022_Sci.Total.Environ__160909
PubMedID: 36526185

Title : Meta-analysis of clinical efficacy and safety of Yangxuenao Granules combined with cholinesterase inhibitors in the treatment of vascular cognitive impairment -
Author(s) : Peng C , Zhou D
Ref : Minerva Med , : , 2022
PubMedID: 36178047

Title : Oxidative stress and detoxification mechanisms of earthworms (Eisenia fetida) after exposure to flupyradifurone in a soil-earthworm system - Qiao_2022_J.Environ.Manage_322_115989
Author(s) : Qiao Z , Li P , Tan J , Peng C , Zhang F , Zhang W , Jiang X
Ref : J Environ Manage , 322 :115989 , 2022
Abstract : Flupyradifurone (FLU) has great application potential in agricultural production as a new generation of neonicotinoid insecticide after imidacloprid. Nevertheless, the toxic effects of FLU on non-target soil organisms remain unclear, resulting in considerable environmental risks. We evaluated the acute and subchronic toxicities of FLU to earthworms. The results of acute toxicity show that the median lethal concentration (LC(50)) values (14 d) of FLU were 186.9773 mg kg(-1) for adult earthworms and 157.6502 mg kg(-1) for juveniles, respectively. The subchronic toxicity of FLU that focused on the activities of antioxidant and detoxication enzymes showed the superoxide dismutase (SOD), catalase (CAT), and glutathione-S transferase (GST) activities in earthworms increased while the peroxidase (POD) and acetylcholinesterase (AChE) activities decreased after exposure to FLU. Oxidative damage analyses revealed that the reactive oxygen species (ROS) level and malonaldehyde (MDA) content in earthworms were increased by FLU, resulting in DNA damage. Transcriptomics and RT-qPCR confirmed that FLU influenced the expression of genes related to antioxidant response and detoxification of earthworms. Ultimately detoxification metabolism, environmental information processing, cell processes, and immune system pathways are significantly enriched to respond jointly to FLU. Our study fills the gaps in the toxicity of FLU to earthworms, providing a basis for its risk assessment of soil ecosystems and non-target biological toxicity.
ESTHER : Qiao_2022_J.Environ.Manage_322_115989
PubMedSearch : Qiao_2022_J.Environ.Manage_322_115989
PubMedID: 36055090

Title : RNAi Mediated Gene Silencing of Detoxification Related Genes in the Ectropis oblique - Peng_2022_Genes.(Basel)_13_
Author(s) : Peng C , Yin H , Liu Y , Mao XF , Liu ZY
Ref : Genes (Basel) , 13 : , 2022
Abstract : Ectropis oblique is one of the main pests that feed on tea leaves. At present, the main control method is chemical control, but the long-term use of insecticides has been related to the development of insect resistance. One of the resistance mechanisms is the upregulation of relevant detoxification enzymes for defense. In this study, four genes with increased expression were screened from the gene sequences annotated from the transcriptome data of deltamethrin-treated larvae of E. oblique, which are acid phosphatase EoACP138, and cytochrome P450 EoCYP316, carboxylesterase EoCarE592 and acetylcholine esterase EoAchE989, respectively. The fourth instar larvae of E. oblique were stimulated by deltamethrin, chlorpyrifos and fenpropathrin respectively, and the expression levels of the genes were detected by qRT-PCR. The result showed that all four genes' expression had significantly increased under the stimulation of three insecticides. RNAi technology was used to silence the expression of genes of EoACP138, EoCYP316, EoCarE592 and EoAchE989 in the fourth instar larvae of E. oblique. The change in the expression levels of the above genes in the larvae treated with dsRNA and stimulated with pesticides was determined by qRT-PCR. The target genes have been effectively silenced after feeding on dsRNA and higher sensitivity with higher mortality to pesticides was observed in the larvae interfered with dsRNA. The above genes are related to the detoxification and metabolism of resistance of E. oblique, which lays a foundation for further study on the mechanism of insecticide resistance in E. oblique.
ESTHER : Peng_2022_Genes.(Basel)_13_
PubMedSearch : Peng_2022_Genes.(Basel)_13_
PubMedID: 35885924

Title : Distal mutation V486M disrupts the catalytic activity of DPP4 by affecting the flap of the propeller domain - Li_2021_Acta.Pharmacol.Sin__1
Author(s) : Li TT , Peng C , Wang JQ , Xu ZJ , Su MB , Li J , Zhu WL , Li JY
Ref : Acta Pharmacol Sin , :1 , 2021
Abstract : Dipeptidyl peptidase-4 (DPP4) plays a crucial role in regulating the bioactivity of glucagon-like peptide-1 (GLP-1) that enhances insulin secretion and pancreatic beta-cell proliferation, making it a therapeutic target for type 2 diabetes. Although the crystal structure of DPP4 has been determined, its structure-function mechanism is largely unknown. Here, we examined the biochemical properties of sporadic human DPP4 mutations distal from its catalytic site, among which V486M ablates DPP4 dimerization and causes loss of enzymatic activity. Unbiased molecular dynamics simulations revealed that the distal V486M mutation induces a local conformational collapse in a beta-propeller loop (residues 234-260, defined as the flap) and disrupts the dimerization of DPP4. The "open/closed" conformational transitions of the flap whereby capping the active site, are involved in the enzymatic activity of DPP4. Further site-directed mutagenesis guided by theoretical predictions verified the importance of the conformational dynamics of the flap for the enzymatic activity of DPP4. Therefore, the current studies that combined theoretical modeling and experimental identification, provide important insights into the biological function of DPP4 and allow for the evaluation of directed DPP4 genetic mutations before initiating clinical applications and drug development.
ESTHER : Li_2021_Acta.Pharmacol.Sin__1
PubMedSearch : Li_2021_Acta.Pharmacol.Sin__1
PubMedID: 34907358

Title : Physiological and transcriptomic changes of zebrafish (Danio rerio) embryos-larvae in response to 2-MIB exposure - Zhou_2021_J.Hazard.Mater_416_126142
Author(s) : Zhou W , Li X , Wang Y , Wang J , Zhang J , Wei H , Peng C , Wang Z , Li G , Li D
Ref : J Hazard Mater , 416 :126142 , 2021
Abstract : 2-Methylisoborneol (2-MIB), a natural odorous substance, is widely distributed in water environment, but there is a paucity of information concerning its systemic toxicity. Herein, we investigated the effects of 2-MIB exposure on developmental parameters, locomotive behavior, oxidative stress, apoptosis and transcriptome of zebrafish. Zebrafish embryos exposed to different concentrations (0, 0.5, 5 and 42.8 microg/L) of 2-MIB showed no changes in mortality, hatchability, and malformation rate, but the body length of zebrafish larvae was significantly increased in a dose-dependent manner, and accompanied by the changes of growth hormone/insulin-like growth factor (GH/IGF) axis and the hypothalamic-pituitary-thyroid (HPT) axis genes. Moreover, the swimming activity of zebrafish larvae increased, which may be due to the increase of acetylcholinesterase (AChE) activity. Meanwhile, 2-MIB caused oxidative stress and apoptosis in zebrafish larvae by altering the NF-E2-related factor 2 (Nrf2) and mitochondrial signaling pathways, respectively. Transcriptome sequencing assay showed that the phototransduction signaling pathway was significantly enriched, and most of the genes in this pathway exhibited enhanced expression after exposure to 2-MIB. These findings provide an important reference for risk assessment and early warning to 2-MIB exposure.
ESTHER : Zhou_2021_J.Hazard.Mater_416_126142
PubMedSearch : Zhou_2021_J.Hazard.Mater_416_126142
PubMedID: 34492931

Title : Tunicyclin L, a cyclic peptide from Psammosilene tunicoides: Isolation, characterization, conformational studies and biological activity - Hou_2020_Fitoterapia__104628
Author(s) : Hou Y , Wang M , Sun C , Peng C , Zhang Y , Li X
Ref : Fitoterapia , :104628 , 2020
Abstract : Tunicyclin L (1), cyclo (L-Pro(1)-Gly-L-Phe(1)-L-Ile-L-Pro(2)-L-Phe -L-Thr-L-Val), and 11 known compounds, including one cyclic peptide (2), eight carboline alkaloids (3-10), one lignan (11) and one flavone (12) were isolated from the roots of Psammosilene tunicoides. Their structures were elucidated on the basis of extensive UV, IR, MS, NMR spectroscopic data and comparison with literature. Single-crystal X-ray diffraction results revealed the stereochemistry of the 24-membered ring cyclic peptide (1). Among these known compounds, compound 6 was found to be a new natural product, and compounds 3, 4, and 11 were isolated from this plant for the first time. Five compounds (1, 3, 4, 7, and 9) showed moderate anti-acetylcholinesterase (AChE) activity.
ESTHER : Hou_2020_Fitoterapia__104628
PubMedSearch : Hou_2020_Fitoterapia__104628
PubMedID: 32433930

Title : Identification of Highly Selective Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Inhibitors by a Covalent Fragment-Based Approach - Huang_2020_J.Med.Chem_63_7052
Author(s) : Huang F , Hu H , Wang K , Peng C , Xu W , Zhang Y , Gao J , Liu Y , Zhou H , Huang R , Li M , Shen J , Xu Y
Ref : Journal of Medicinal Chemistry , 63 :7052 , 2020
Abstract : Covalent ligands are of great interest as therapeutic drugs or biochemical tools. Here, we reported the discovery of highly selective and irreversible inhibitors of lipoprotein-associated phospholipase A2 (Lp-PLA2) using a covalent fragment-based approach. The crystal structure of Lp-PLA2 in complex with a covalent fragment not only reveals the covalent reaction mechanism but also provides a good starting point to design compound 8, which has a more than 130,000-fold and 3900-fold increase in potency and selectivity, respectively, compared to those of the covalent fragment. Furthermore, fluorescent probes with high selectivity and sensitivity are developed to characterize Lp-PLA2 and its enzymatic activity in vitro or even in living cells in a way more convenient than immunoblotting tests or immunofluorescence imaging. Overall, we provide a paradigm for application of the covalent fragment-based strategy in covalent ligand discovery and the advantage of enol-cyclocarbamate as a new warhead in designing covalent inhibitors of serine hydrolases.
ESTHER : Huang_2020_J.Med.Chem_63_7052
PubMedSearch : Huang_2020_J.Med.Chem_63_7052
PubMedID: 32459096
Gene_locus related to this paper: human-PLA2G7

Title : Identification, characterization and expression analyses of cholinesterases genes in Yesso scallop (Patinopecten yessoensis) reveal molecular function allocation in responses to ocean acidification - Xing_2020_Aquat.Toxicol_231_105736
Author(s) : Xing Q , Liao H , Peng C , Zheng G , Yang Z , Wang J , Lu W , Huang X , Bao Z
Ref : Aquat Toxicol , 231 :105736 , 2020
Abstract : Cholinesterases are key enzymes in central and peripheral cholinergic nerve system functioning on nerve impulse transmission in animals. Though cholinesterases have been identified in most vertebrates, the knowledge about the variable numbers and multiple functions of the genes is still quite meagre in invertebrates, especially in scallops. In this study, the complete cholinesterase (ChE) family members have been systematically characterized in Yesso scallop (Patinopecten yessoensis) via whole-genome scanning through in silico analysis. Ten ChE family members in the genome of Yesso scallop (designated PyChEs) were identified and potentially acted to be the largest number of ChE in the reported species to date. Phylogenetic and protein structural analyses were performed to determine the identities and evolutionary relationships of these genes. The expression profiles of PyChEs were determined in all developmental stages, in healthy adult tissues, and in mantles under low pH stress (pH 6.5 and 7.5). Spatiotemporal expression suggested the ubiquitous functional roles of PyChEs in all stages of development, as well as general and tissue-specific functions in scallop tissues. Regulation expressions revealed diverse up- and down-regulated expression patterns at most time points, suggesting different functional specialization of gene superfamily members in response to ocean acidification (OA). Evidences in gene number, phylogenetic relationships and expression patterns of PyChEs revealed that functional innovations and differentiations after gene duplication may result in altered functional constraints among PyChEs gene clusters. Collectively, our results provide the potential clues that the selection pressures coming from the environment were the potential inducement leading to function allocation of ChE family members in scallop.
ESTHER : Xing_2020_Aquat.Toxicol_231_105736
PubMedSearch : Xing_2020_Aquat.Toxicol_231_105736
PubMedID: 33422860
Gene_locus related to this paper: mizye-a0a210qls6 , mizye-a0a210qis3 , mizye-a0a210qg00 , mizye-a0a210r5n9 , mizye-a0a210qbv2 , mizye-a0a210pu25 , mizye-a0a210ptr6 , mizye-a0a210ptv1 , mizye-a0a210ptq0 , mizye-P021348901.2

Title : A Review of the Pharmacological Properties of Psoralen - Ren_2020_Front.Pharmacol_11_571535
Author(s) : Ren Y , Song X , Tan L , Guo C , Wang M , Liu H , Cao Z , Li Y , Peng C
Ref : Front Pharmacol , 11 :571535 , 2020
Abstract : Psoralen is the principal bioactive component in the dried fruits of Cullen corylifolium (L.) Medik (syn. Psoralea corylifolia L), termed "Buguzhi" in traditional Chinese medicine (TCM). Recent studies have demonstrated that psoralen displays multiple bioactive properties, beneficial for the treatment of osteoporosis, tumors, viruses, bacteria, and inflammation. The present review focuses on the research evidence relating to the properties of psoralen gathered over recent years. Firstly, multiple studies have demonstrated that psoralen exerts strong anti-osteoporotic effects via regulation of osteoblast/osteoclast/chondrocyte differentiation or activation due to the participation in multiple molecular mechanisms of the wnt/beta-catenin, bone morphogenetic protein (BMP), inositol-requiring enzyme 1 (IRE1)/apoptosis signaling kinase 1 (ASK1)/c-jun N-terminal kinase (JNK) and the Protein Kinase B(AKT)/activator protein-1 (AP-1) axis, and the expression of miR-488, peroxisome proliferators-activated receptor-gamma (PPARgamma), and matrix metalloproteinases (MMPs). In addition, the antitumor properties of psoralen are associated with the induction of ER stress-related cell death via enhancement of PERK: Pancreatic Endoplasmic Reticulum Kinase (PERK)/activating transcription factor (ATF), 78kD glucose-regulated protein (GRP78)/C/EBP homologous protein (CHOP), and 94kD glucose-regulated protein (GRP94)/CHOP signaling, and inhibition of P-glycoprotein (P-gp) or ATPase that overcomes multidrug resistance. Furthermore, multiple articles have shown that the antibacterial, anti-inflammatory and neuroprotective effects of psoralen are a result of its interaction with viral polymerase (Pol), destroying the formation of biofilm, and regulating the activation of tumor necrosis factor alpha (TNF-alpha), transforming growth factor beta (TGF-beta), interleukin 4/5/6/8/12/13 (IL-4/5/6/8/12/13), GATA-3, acetylcholinesterase (AChE), and the hypothalamic-pituitary-adrenal (HPA) axis. Finally, the toxic effects and mechanisms of action of psoralen have also been reviewed.
ESTHER : Ren_2020_Front.Pharmacol_11_571535
PubMedSearch : Ren_2020_Front.Pharmacol_11_571535
PubMedID: 33013413

Title : Discovery of Novel Bat Coronaviruses in South China That Use the Same Receptor as Middle East Respiratory Syndrome Coronavirus - Luo_2018_J.Virol_92_
Author(s) : Luo CM , Wang N , Yang XL , Liu HZ , Zhang W , Li B , Hu B , Peng C , Geng QB , Zhu GJ , Li F , Shi ZL
Ref : J Virol , 92 : , 2018
Abstract : Middle East respiratory syndrome coronavirus (MERS-CoV) has represented a human health threat since 2012. Although several MERS-related CoVs that belong to the same species as MERS-CoV have been identified from bats, they do not use the MERS-CoV receptor, dipeptidyl peptidase 4 (DPP4). Here, we screened 1,059 bat samples from at least 30 bat species collected in different regions in south China and identified 89 strains of lineage C betacoronaviruses, including Tylonycteris pachypus coronavirus HKU4, Pipistrellus pipistrelluscoronavirus HKU5, and MERS-related CoVs. We sequenced the full-length genomes of two positive samples collected from the great evening bat, Ia io, from Guangdong Province. The two genomes were highly similar and exhibited genomic structures identical to those of other lineage C betacoronaviruses. While they exhibited genome-wide nucleotide identities of only 75.3 to 81.2% with other MERS-related CoVs, their gene-coding regions were highly similar to their counterparts, except in the case of the spike proteins. Further protein-protein interaction assays demonstrated that the spike proteins of these MERS-related CoVs bind to the receptor DPP4. Recombination analysis suggested that the newly discovered MERS-related CoVs have acquired their spike genes from a DPP4-recognizing bat coronavirus HKU4. Our study provides further evidence that bats represent the evolutionary origins of MERS-CoV.IMPORTANCE Previous studies suggested that MERS-CoV originated in bats. However, its evolutionary path from bats to humans remains unclear. In this study, we discovered 89 novel lineage C betacoronaviruses in eight bat species. We provide evidence of a MERS-related CoV derived from the great evening bat that uses the same host receptor as human MERS-CoV. This virus also provides evidence for a natural recombination event between the bat MERS-related CoV and another bat coronavirus, HKU4. Our study expands the host ranges of MERS-related CoV and represents an important step toward establishing bats as the natural reservoir of MERS-CoV. These findings may lead to improved epidemiological surveillance of MERS-CoV and the prevention and control of the spread of MERS-CoV to humans.
ESTHER : Luo_2018_J.Virol_92_
PubMedSearch : Luo_2018_J.Virol_92_
PubMedID: 29669833

Title : Thiolation Protein-Based Transfer of Indolyl to a Ribosomally Synthesized Polythiazolyl Peptide Intermediate during the Biosynthesis of the Side-Ring System of Nosiheptide - Qiu_2017_J.Am.Chem.Soc_139_18186
Author(s) : Qiu Y , Du Y , Zhang F , Liao R , Zhou S , Peng C , Guo Y , Liu W
Ref : Journal of the American Chemical Society , 139 :18186 , 2017
Abstract : Nosiheptide, a potent bicyclic member of the family of thiopeptide antibiotics, possesses a distinctive l-Trp-derived indolyl moiety. The way in which this moiety is incorporated into a ribosomally synthesized and post-translationally modified thiopeptide remains poorly understood. Here, we report that NosK, an alpha/beta-hydrolase fold protein, mediates the transfer of indolyl from NosJ, a discrete thiolation protein, to a linear pentathiazolyl peptide intermediate rather than its genetically encoded untreated precursor. This intermediate results from enzymatic processing of the peptide precursor, in which five of the six l-Cys residues are transformed into thiazoles but Cys4 selectively remains unmodified for indolyl substitution via a thioester exchange. Determining the timing of indolyl incorporation, which expands the chemical space of a thiopeptide framework, facilitates mechanistic access to the unusual logic of post-translational modifications in the biosynthesis of nosiheptide-type thiopeptide members that share a similar compact side-ring system.
ESTHER : Qiu_2017_J.Am.Chem.Soc_139_18186
PubMedSearch : Qiu_2017_J.Am.Chem.Soc_139_18186
PubMedID: 29200275
Gene_locus related to this paper: stras-c6fx50

Title : Lipase adsorption on different nanomaterials: a multi-scale simulation study - Zhao_2015_Phys.Chem.Chem.Phys_17_840
Author(s) : Zhao D , Peng C , Zhou J
Ref : Phys Chem Chem Phys , 17 :840 , 2015
Abstract : Candida antarctica lipase B (CalB) is an efficient biocatalyst for hydrolysis and esterification, which plays an important role in the production of biodiesel in the bioenergy industries. The ordered immobilisation of lipases on different supports would be significant for its enzymatic catalysis in some biodiesel production processes; however, the underlying mechanisms and the preferred lipase orientation are not well understood yet. In this work, a fundamental understanding of the orientation and adsorption mechanism of lipase on four different nanomaterial surfaces with different surface chemistry are explored in detail by a combination of parallel tempering Monte Carlo (PTMC) and molecular dynamics (MD) simulations. Simulation results show that lipase is strongly adsorbed onto the hydrophobic graphite surface, as reflected by the large contact area and interaction energy; while the adsorption onto the hydrophilic TiO2 surface is weak due to two strongly adhered water layers; meanwhile lipase undergoes desorption and reorientation processes. For CalB adsorption on positively and negatively charged surfaces (NH2-SAM and COOH-SAM), the orientation distributions of lipase are narrow, and opposite orientations are obtained. CalB adsorbed on NH2-SAM has its catalytic centre oriented towards the surface, which is not conducive to the substrate binding; while the catalytic centre faces toward the solution when it is adsorbed on the COOH-SAM. Besides, the native structures of CalB adsorbed on different surfaces are preserved, which indicates lipase as a robust enzyme. The simulation results will promote our understanding on how surface properties of nanomaterials, such as charge or hydrophobicity, will affect lipase immobilisation, and help us in the rational design and development of immobilised lipase carriers.
ESTHER : Zhao_2015_Phys.Chem.Chem.Phys_17_840
PubMedSearch : Zhao_2015_Phys.Chem.Chem.Phys_17_840
PubMedID: 25412148

Title : Molecular Simulation Study of Feruloyl Esterase Adsorption on Charged Surfaces: Effects of Surface Charge Density and Ionic Strength - Liu_2015_Langmuir_31_10751
Author(s) : Liu J , Peng C , Yu G , Zhou J
Ref : Langmuir , 31 :10751 , 2015
Abstract : The surrounding conditions, such as surface charge density and ionic strength, play an important role in enzyme adsorption. The adsorption of a nonmodular type-A feruloyl esterase from Aspergillus niger (AnFaeA) on charged surfaces was investigated by parallel tempering Monte Carlo (PTMC) and all-atom molecular dynamics (AAMD) simulations at different surface charge densities (+/-0.05 and +/-0.16 C.m(-2)) and ionic strengths (0.007 and 0.154 M). The adsorption energy, orientation, and conformational changes were analyzed. Simulation results show that whether AnFaeA can adsorb onto a charged surface is mainly controlled by electrostatic interactions between AnFaeA and the charged surface. The electrostatic interactions between AnFaeA and charged surfaces are weakened when the ionic strength increases. The positively charged surface at low surface charge density and high ionic strength conditions can maximize the utilization of the immobilized AnFaeA. The counterion layer plays a key role in the adsorption of AnFaeA on the negatively charged COOH-SAM. The native conformation of AnFaeA is well preserved under all of these conditions. The results of this work can be used for the controlled immobilization of AnFaeA.
ESTHER : Liu_2015_Langmuir_31_10751
PubMedSearch : Liu_2015_Langmuir_31_10751
PubMedID: 26379082

Title : Genome and transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. cubense causing banana vascular wilt disease - Guo_2014_PLoS.One_9_e95543
Author(s) : Guo L , Han L , Yang L , Zeng H , Fan D , Zhu Y , Feng Y , Wang G , Peng C , Jiang X , Zhou D , Ni P , Liang C , Liu L , Wang J , Mao C , Fang X , Peng M , Huang J
Ref : PLoS ONE , 9 :e95543 , 2014
Abstract : BACKGROUND: The asexual fungus Fusarium oxysporum f. sp. cubense (Foc) causing vascular wilt disease is one of the most devastating pathogens of banana (Musa spp.). To understand the molecular underpinning of pathogenicity in Foc, the genomes and transcriptomes of two Foc isolates were sequenced. METHODOLOGY/PRINCIPAL FINDINGS: Genome analysis revealed that the genome structures of race 1 and race 4 isolates were highly syntenic with those of F. oxysporum f. sp. lycopersici strain Fol4287. A large number of putative virulence associated genes were identified in both Foc genomes, including genes putatively involved in root attachment, cell degradation, detoxification of toxin, transport, secondary metabolites biosynthesis and signal transductions. Importantly, relative to the Foc race 1 isolate (Foc1), the Foc race 4 isolate (Foc4) has evolved with some expanded gene families of transporters and transcription factors for transport of toxins and nutrients that may facilitate its ability to adapt to host environments and contribute to pathogenicity to banana. Transcriptome analysis disclosed a significant difference in transcriptional responses between Foc1 and Foc4 at 48 h post inoculation to the banana 'Brazil' in comparison with the vegetative growth stage. Of particular note, more virulence-associated genes were up regulated in Foc4 than in Foc1. Several signaling pathways like the mitogen-activated protein kinase Fmk1 mediated invasion growth pathway, the FGA1-mediated G protein signaling pathway and a pathogenicity associated two-component system were activated in Foc4 rather than in Foc1. Together, these differences in gene content and transcription response between Foc1 and Foc4 might account for variation in their virulence during infection of the banana variety 'Brazil'. CONCLUSIONS/SIGNIFICANCE: Foc genome sequences will facilitate us to identify pathogenicity mechanism involved in the banana vascular wilt disease development. These will thus advance us develop effective methods for managing the banana vascular wilt disease, including improvement of disease resistance in banana.
ESTHER : Guo_2014_PLoS.One_9_e95543
PubMedSearch : Guo_2014_PLoS.One_9_e95543
PubMedID: 24743270
Gene_locus related to this paper: fusox-w9hvf0 , fusox-x0d9n6

Title : Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes - You_2014_Nat.Commun_5_5594
Author(s) : You X , Bian C , Zan Q , Xu X , Liu X , Chen J , Wang J , Qiu Y , Li W , Zhang X , Sun Y , Chen S , Hong W , Li Y , Cheng S , Fan G , Shi C , Liang J , Tom Tang Y , Yang C , Ruan Z , Bai J , Peng C , Mu Q , Lu J , Fan M , Yang S , Huang Z , Jiang X , Fang X , Zhang G , Zhang Y , Polgar G , Yu H , Li J , Liu Z , Ravi V , Coon SL , Yang H , Venkatesh B , Shi Q
Ref : Nat Commun , 5 :5594 , 2014
Abstract : Mudskippers are amphibious fishes that have developed morphological and physiological adaptations to match their unique lifestyles. Here we perform whole-genome sequencing of four representative mudskippers to elucidate the molecular mechanisms underlying these adaptations. We discover an expansion of innate immune system genes in the mudskippers that may provide defence against terrestrial pathogens. Several genes of the ammonia excretion pathway in the gills have experienced positive selection, suggesting their important roles in mudskippers' tolerance to environmental ammonia. Some vision-related genes are differentially lost or mutated, illustrating genomic changes associated with aerial vision. Transcriptomic analyses of mudskippers exposed to air highlight regulatory pathways that are up- or down-regulated in response to hypoxia. The present study provides a valuable resource for understanding the molecular mechanisms underlying water-to-land transition of vertebrates.
ESTHER : You_2014_Nat.Commun_5_5594
PubMedSearch : You_2014_Nat.Commun_5_5594
PubMedID: 25463417
Gene_locus related to this paper: 9gobi-a0a3b4bh68 , 9gobi-a0a3b4bmj6 , 9gobi-a0a3b4alj9 , 9gobi-a0a3b4biy6 , 9gobi-a0a3b4ah01 , 9gobi-a0a3b3z8m7 , 9gobi-a0a3b4aaj5 , 9gobi-a0a3b4b6y7

Title : Multiple Modes of alpha7 nAChR Noncompetitive Antagonism of Control Agonist-Evoked and Allosterically Enhanced Currents - Peng_2013_Mol.Pharmacol_84_459
Author(s) : Peng C , Kimbrell MR , Tian C , Pack TF , Crooks PA , Fifer EK , Papke RL
Ref : Molecular Pharmacology , 84 :459 , 2013
Abstract : Positive allosteric modulators (PAMs) of alpha7 nicotinic acetylcholine receptors can enhance ion channel currents and downstream effects of alpha7 stimulation. We investigated the approach of using noncompetitive antagonists to regulate alpha7 receptor function, potentially distinguishing effects requiring ion channel currents from signaling induced by nonconducting states. Three small readily reversible antagonists, (1S,2R,4R)-N,2,3,3-tetramethylbicyclo[2.2.1]heptan-2-amine (mecamylamine), N-(2.6-dimethylphenylcarbamoylmethyl)triethylammonium bromide (QX-314), and 2-(dimethylamino)ethyl 4-(butylamino)benzoate (tetracaine), as well as three large slowly reversible antagonists, bis-(2,2,6,6-tetramethyl-4-piperidinyl) sebacate (BTMPS), 2,2,6,6-tetramethylpiperidin-4-yl heptanoate (TMPH), and 1,2,4,5-tetra-{5-[1-(3-benzyl)pyridinium]pent-1-yl}benzene tetrabromide (tkP3BzPB), were investigated for their effectiveness and voltage dependence in the inhibition of responses evoked by acetylcholine alone or augmented by the alpha7-selective PAM N-(5-chloro-2,4-dimethoxyphenyl)-N'-(5-methyl-3-isoxazolyl)-urea (PNU-120596). Analyses of the small antagonists on PNU-120596-potentiated single-channel bursts indicated that each agent had a distinct mechanism of inhibition and only that of QX-314 was consistent with simple open channel block. In addition to decreasing channel open times and burst durations, mecamylamine and tetracaine induced unique subconductance states. To determine whether channel-blocking activity alone would be sufficient to prevent cell death, the antagonists were tested for their ability to protect alpha7-expressing cells from cytotoxic effects of the alpha7 agonist choline in combination with PNU-120596. Only tetracaine and tkP3BzPB, the two agents that had effects least consistent with simple ion channel block, were fully cytoprotective at concentrations that gave submaximal inhibition of macroscopic currents in oocytes. Further analyses indicated that toxicity produced by PNU-120596 and choline was calcium independent and likely an apoptotic event. Our results are consistent with the hypothesis that PAMs may modulate conformational states important for both channel activity and ion channel-independent signaling.
ESTHER : Peng_2013_Mol.Pharmacol_84_459
PubMedSearch : Peng_2013_Mol.Pharmacol_84_459
PubMedID: 23839567

Title : Differential modulation of brain nicotinic acetylcholine receptor function by cytisine, varenicline, and two novel bispidine compounds: emergent properties of a hybrid molecule - Peng_2013_J.Pharmacol.Exp.Ther_347_424
Author(s) : Peng C , Stokes C , Mineur YS , Picciotto MR , Tian C , Eibl C , Tomassoli I , Guendisch D , Papke RL
Ref : Journal of Pharmacology & Experimental Therapeutics , 347 :424 , 2013
Abstract : Partial agonist therapies for the treatment of nicotine addiction and dependence depend on both agonistic and antagonistic effects of the ligands, and side effects associated with other nAChRs greatly limit the efficacy of nicotinic partial agonists. We evaluated the in vitro pharmacological properties of four partial agonists, two current smoking cessation drugs, varenicline and cytisine, and two novel bispidine compounds, BPC and BMSP, by using defined nAChR subtypes expressed in Xenopus laevis oocytes and human embryonic kidney 293 cells. Similar to varenicline and cytisine, BPC and BMSP are partial agonists of alpha4beta2 nAChRs, although BMSP produced very little activation of these receptors. Unlike varenicline and cytisine, BPC and BMSP showed desired low activity. BPC produced mecamylamine-sensitive steady-state activation of alpha4* receptors that was not evident with BMSP. We evaluated the modulation of alpha4*- and alpha7-mediated responses in rat lateral geniculate nucleus (LGN) neurons and hippocampal stratum radiatum (SR) interneurons, respectively. The LGN neurons were sensitive to a very low concentration of varenicline, and the SR interneuron responses were also sensitive to varenicline at a submicromolar concentration. Although 300 nM BPC strongly inhibited the ACh-evoked responses of LGN neurons, it did not inhibit the alpha7 currents of SR interneurons. Similar results were observed with 300 nM BMSP. Additionally, the bispidine compounds were efficacious in the mouse tail suspension test, demonstrating that they affect receptors in the brain when delivered systemically. Our data indicate that BPC and BMSP are promising alpha4beta2* partial agonists for pharmacotherapeutics.
ESTHER : Peng_2013_J.Pharmacol.Exp.Ther_347_424
PubMedSearch : Peng_2013_J.Pharmacol.Exp.Ther_347_424
PubMedID: 23959137

Title : Assessment of activities and conformation of lipases treated with sub- and supercritical carbon dioxide - Chen_2013_Appl.Biochem.Biotechnol_169_2189
Author(s) : Chen D , Peng C , Zhang H , Yan Y
Ref : Appl Biochem Biotechnol , 169 :2189 , 2013
Abstract : In order to illustrate the underlining mechanism of the effect of high pressure on lipases from different resources, the influence of compressed carbon dioxide treatment on the esterification activities and conformation of the three lipases Candida rugosa lipase (CRL), Pseudomonas fluorescens lipase, and Rhizopus oryzae lipase was investigated in the present work. The results showed that the lipases activities were significantly enhanced in most of high-pressure treatments, except the pressure had a negative effect on CRL activity in supercritical condition. Mild depressurization rate could remain the lipase's activity by protecting its rigid structure under supercritical fluid. Conformational analysis by Fourier transform-infrared spectrometry and fluorescence emission spectra revealed that the variances of lipase activity after high-pressure treatment were correlated with the changes of its alpha-helix content and fluorescence intensity. Additionally, transesterification catalyzed by three lipases in supercritical carbon dioxide were conducted, and 87.2 % biodiesel conversion was obtained by CRL after 3 h, resulting in a great reduction of reaction time.
ESTHER : Chen_2013_Appl.Biochem.Biotechnol_169_2189
PubMedSearch : Chen_2013_Appl.Biochem.Biotechnol_169_2189
PubMedID: 23417391

Title : Intrinsically low open probability of alpha7 nicotinic acetylcholine receptors can be overcome by positive allosteric modulation and serum factors leading to the generation of excitotoxic currents at physiological temperatures - Williams_2012_Mol.Pharmacol_82_746
Author(s) : Williams DK , Peng C , Kimbrell MR , Papke RL
Ref : Molecular Pharmacology , 82 :746 , 2012
Abstract : alpha7 nicotinic acetylcholine receptors (nAChRs) have been a puzzle since their discovery in brain and non-neuronal tissues. Maximal transient probability of an alpha7 nAChR being open with rapid agonist applications is only 0.002. The concentration dependence of alpha7 responses measured from transfected cells and Xenopus laevis oocytes shows the same disparity in potency estimations for peak currents and net charge, despite being studied at 1000-fold different time scales. In both cases the EC(5)(0) was approximately 10-fold lower for net charge than for peak currents. The equivalence of the data obtained at such disparate time scales indicates that desensitization of alpha7 is nearly instantaneous. At high levels of agonist occupancy, the receptor is preferentially converted to a ligand-bound nonconducting state, which can be destabilized by the positive allosteric modulator N-(5-chloro-2,4-dimethoxyphenyl)-N'-(5-methyl-3-isoxazolyl)-urea (PNU-120596). Such currents can be sufficiently large to be cytotoxic to the alpha7-expressing cells. Both the potentiating effect of PNU-120596 and the associated cytotoxicity have a high temperature dependence that can be compensated for by serum factors. Therefore, despite reduced potentiation at body temperatures, use of type II positive allosteric modulators may put cells that naturally express high levels of alpha7 nAChRs, such as neurons in the hippocampus and hypothalamus, at risk. With a low intrinsic open probability and high propensity toward the induction of nonconducting ligand-bound states, it is likely that the well documented regulation of signal transduction pathways by alpha7 nAChRs in cells such as those that regulate inflammation may be independent of ion channel activation and associated with the nonconducting conformational states.
ESTHER : Williams_2012_Mol.Pharmacol_82_746
PubMedSearch : Williams_2012_Mol.Pharmacol_82_746
PubMedID: 22828799

Title : The oyster genome reveals stress adaptation and complexity of shell formation - Zhang_2012_Nature_490_49
Author(s) : Zhang G , Fang X , Guo X , Li L , Luo R , Xu F , Yang P , Zhang L , Wang X , Qi H , Xiong Z , Que H , Xie Y , Holland PW , Paps J , Zhu Y , Wu F , Chen Y , Wang J , Peng C , Meng J , Yang L , Liu J , Wen B , Zhang N , Huang Z , Zhu Q , Feng Y , Mount A , Hedgecock D , Xu Z , Liu Y , Domazet-Loso T , Du Y , Sun X , Zhang S , Liu B , Cheng P , Jiang X , Li J , Fan D , Wang W , Fu W , Wang T , Wang B , Zhang J , Peng Z , Li Y , Li N , Chen M , He Y , Tan F , Song X , Zheng Q , Huang R , Yang H , Du X , Chen L , Yang M , Gaffney PM , Wang S , Luo L , She Z , Ming Y , Huang W , Huang B , Zhang Y , Qu T , Ni P , Miao G , Wang Q , Steinberg CE , Wang H , Qian L , Liu X , Yin Y
Ref : Nature , 490 :49 , 2012
Abstract : The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.
ESTHER : Zhang_2012_Nature_490_49
PubMedSearch : Zhang_2012_Nature_490_49
PubMedID: 22992520
Gene_locus related to this paper: cragi-k1qzk7 , cragi-k1rad0 , cragi-k1p6v9 , cragi-k1pa46 , cragi-k1pga2 , cragi-k1pp63 , cragi-k1pwa8 , cragi-k1q0b1.1 , cragi-k1q0b1.2 , cragi-k1q1h2 , cragi-k1q2z6 , cragi-k1qaj8 , cragi-k1qaw5 , cragi-k1qhl5 , cragi-k1qly1 , cragi-k1qqb1.1 , cragi-k1qqb1.2 , cragi-k1qs61 , cragi-k1qs99 , cragi-k1qwl6 , cragi-k1r068 , cragi-k1r0n3.1 , cragi-k1r0n3.2 , cragi-k1r0r4 , cragi-k1r1i9 , cragi-k1r8q9 , cragi-k1rgi1 , cragi-k1rig4 , cragi-k1s0a7.1 , cragi-k1s0a7.2 , cragi-k1s0a7.3 , cragi-k1q6q0 , cragi-k1rru1 , cragi-k1qfi4 , cragi-k1qvm5 , cragi-k1qq58 , cragi-k1qdc0 , cragi-k1r754 , cragi-k1pje5 , cragi-k1qca6 , cragi-k1qdt5 , cragi-k1qkz7 , cragi-k1rgd2 , cragi-k1puh6 , cragi-k1raz4 , cragi-k1qqj4 , cragi-k1rbs1

Title : Biodiesel synthesis and conformation of lipase from Burkholderia cepacia in room temperature ionic liquids and organic solvents - Liu_2011_Bioresour.Technol_102_10414
Author(s) : Liu Y , Chen D , Yan Y , Peng C , Xu L
Ref : Bioresour Technol , 102 :10414 , 2011
Abstract : Biodiesel synthesis and conformation of Burkholderia cepacia lipase (BCL) were studied in 19 different room temperature ionic liquids (RTLLs) with a range of cation and anion structures. Overall, anion selection had a greater influence on biodiesel conversion than cation choice. RTILs containing Tf2N- and PF6- anions were suitable reaction media, while RTIL of [OmPy][BF4] was the best reaction medium with a biodiesel yield of 82.2+/-1.2%. RTILs with strong water miscible properties showed very low biodiesel yields. Conformational analysis by FT-IR revealed that higher biodiesel conversion in RTILs was correlated with a low tendency in alpha-helix content of BCL. An ultrasound-assisted biocatalysis process in RTILs was used to improve mass transfer rate, leading to 83% reduction of the reaction time for biodiesel production.
ESTHER : Liu_2011_Bioresour.Technol_102_10414
PubMedSearch : Liu_2011_Bioresour.Technol_102_10414
PubMedID: 21955878

Title : Genome sequencing reveals insights into physiology and longevity of the naked mole rat - Kim_2011_Nature_479_223
Author(s) : Kim EB , Fang X , Fushan AA , Huang Z , Lobanov AV , Han L , Marino SM , Sun X , Turanov AA , Yang P , Yim SH , Zhao X , Kasaikina MV , Stoletzki N , Peng C , Polak P , Xiong Z , Kiezun A , Zhu Y , Chen Y , Kryukov GV , Zhang Q , Peshkin L , Yang L , Bronson RT , Buffenstein R , Wang B , Han C , Li Q , Chen L , Zhao W , Sunyaev SR , Park TJ , Zhang G , Wang J , Gladyshev VN
Ref : Nature , 479 :223 , 2011
Abstract : The naked mole rat (Heterocephalus glaber) is a strictly subterranean, extraordinarily long-lived eusocial mammal. Although it is the size of a mouse, its maximum lifespan exceeds 30 years, making this animal the longest-living rodent. Naked mole rats show negligible senescence, no age-related increase in mortality, and high fecundity until death. In addition to delayed ageing, they are resistant to both spontaneous cancer and experimentally induced tumorigenesis. Naked mole rats pose a challenge to the theories that link ageing, cancer and redox homeostasis. Although characterized by significant oxidative stress, the naked mole rat proteome does not show age-related susceptibility to oxidative damage or increased ubiquitination. Naked mole rats naturally reside in large colonies with a single breeding female, the 'queen', who suppresses the sexual maturity of her subordinates. They also live in full darkness, at low oxygen and high carbon dioxide concentrations, and are unable to sustain thermogenesis nor feel certain types of pain. Here we report the sequencing and analysis of the naked mole rat genome, which reveals unique genome features and molecular adaptations consistent with cancer resistance, poikilothermy, hairlessness and insensitivity to low oxygen, and altered visual function, circadian rythms and taste sensing. This information provides insights into the naked mole rat's exceptional longevity and ability to live in hostile conditions, in the dark and at low oxygen. The extreme traits of the naked mole rat, together with the reported genome and transcriptome information, offer opportunities for understanding ageing and advancing other areas of biological and biomedical research.
ESTHER : Kim_2011_Nature_479_223
PubMedSearch : Kim_2011_Nature_479_223
PubMedID: 21993625
Gene_locus related to this paper: hetga-g5amh8 , hetga-g5an68 , hetga-g5anw7 , hetga-g5as32 , hetga-g5atg6 , hetga-g5b5b7 , hetga-g5b9m6 , hetga-g5bdh8 , hetga-g5bmv3 , hetga-g5bp66 , hetga-g5bp67 , hetga-g5bp68 , hetga-g5bpp3 , hetga-g5bsd4 , hetga-g5bul0 , hetga-g5bw29 , hetga-g5bze3 , hetga-g5c6q5 , hetga-g5bfw4 , hetga-g5b832 , hetga-g5c6q8 , hetga-g5bj87 , hetga-a0a0p6jix7 , hetga-g5c108 , hetga-g5c109 , hetga-g5c110 , hetga-g5arh0 , hetga-g5aua1 , hetga-g5are8 , hetga-g5ax31 , hetga-a0a0p6jud6 , hetga-g5b7v3 , hetga-a0a0p6jw61 , hetga-a0a0p6jdl4 , hetga-g5bg83 , hetga-g5bcu5 , hetga-g5bvp0 , hetga-g5b8m7 , hetga-g5b709 , hetga-g5bt99 , hetga-g5b4q4

Title : The genome of the mesopolyploid crop species Brassica rapa - Wang_2011_Nat.Genet_43_1035
Author(s) : Wang X , Wang H , Wang J , Sun R , Wu J , Liu S , Bai Y , Mun JH , Bancroft I , Cheng F , Huang S , Li X , Hua W , Freeling M , Pires JC , Paterson AH , Chalhoub B , Wang B , Hayward A , Sharpe AG , Park BS , Weisshaar B , Liu B , Li B , Tong C , Song C , Duran C , Peng C , Geng C , Koh C , Lin C , Edwards D , Mu D , Shen D , Soumpourou E , Li F , Fraser F , Conant G , Lassalle G , King GJ , Bonnema G , Tang H , Belcram H , Zhou H , Hirakawa H , Abe H , Guo H , Jin H , Parkin IA , Batley J , Kim JS , Just J , Li J , Xu J , Deng J , Kim JA , Yu J , Meng J , Min J , Poulain J , Hatakeyama K , Wu K , Wang L , Fang L , Trick M , Links MG , Zhao M , Jin M , Ramchiary N , Drou N , Berkman PJ , Cai Q , Huang Q , Li R , Tabata S , Cheng S , Zhang S , Sato S , Sun S , Kwon SJ , Choi SR , Lee TH , Fan W , Zhao X , Tan X , Xu X , Wang Y , Qiu Y , Yin Y , Li Y , Du Y , Liao Y , Lim Y , Narusaka Y , Wang Z , Li Z , Xiong Z , Zhang Z
Ref : Nat Genet , 43 :1035 , 2011
Abstract : We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.
ESTHER : Wang_2011_Nat.Genet_43_1035
PubMedSearch : Wang_2011_Nat.Genet_43_1035
PubMedID: 21873998
Gene_locus related to this paper: braol-Q8GTM3 , braol-Q8GTM4 , brarp-m4ei94 , brarp-m4c988 , brana-a0a078j4a9 , brana-a0a078e1m0 , brana-a0a078cd75 , brarp-m4dwa6 , brana-a0a078j4f0 , brana-a0a078cus4 , brana-a0a078f8c2 , brana-a0a078jql1 , brana-a0a078dgj3 , brana-a0a078hw50 , brana-a0a078cuu0 , brana-a0a078dfa9 , brana-a0a078ic91 , brarp-m4ctw3 , brana-a0a078ca65 , brana-a0a078ctc8 , brana-a0a078h021 , brana-a0a078jx23 , brarp-m4da84 , brarp-m4dwr7 , brana-a0a078dh94 , brana-a0a078h612 , brana-a0a078j2t3 , braol-a0a0d3dpb2 , braol-a0a0d3dx76 , brana-a0a078jxa8 , brana-a0a078i2k3 , brarp-m4cwq4 , brarp-m4dcj8 , brarp-m4eh17 , brarp-m4eey4 , brarp-m4dnj8 , brarp-m4ey83 , brarp-m4ey84

Title : Characterization of the saframycin A gene cluster from Streptomyces lavendulae NRRL 11002 revealing a nonribosomal peptide synthetase system for assembling the unusual tetrapeptidyl skeleton in an iterative manner - Li_2008_J.Bacteriol_190_251
Author(s) : Li L , Deng W , Song J , Ding W , Zhao QF , Peng C , Song WW , Tang GL , Liu W
Ref : Journal of Bacteriology , 190 :251 , 2008
Abstract : Saframycin A (SFM-A), produced by Streptomyces lavendulae NRRL 11002, belongs to the tetrahydroisoquinoline family of antibiotics, and its core is structurally similar to the core of ecteinascidin 743, which is a highly potent antitumor drug isolated from a marine tunicate. In this study, the biosynthetic gene cluster for SFM-A was cloned and localized to a 62-kb contiguous DNA region. Sequence analysis revealed 30 genes that constitute the SFM-A gene cluster, encoding an unusual nonribosomal peptide synthetase (NRPS) system and tailoring enzymes and regulatory and resistance proteins. The results of substrate prediction and in vitro characterization of the adenylation specificities of this NRPS system support the hypothesis that the last module acts in an iterative manner to form a tetrapeptidyl intermediate and that the colinearity rule does not apply. Although this mechanism is different from those proposed for the SFM-A analogs SFM-Mx1 and safracin B (SAC-B), based on the high similarity of these systems, it is likely they share a common mechanism of biosynthesis as we describe here. Construction of the biosynthetic pathway of SFM-Y3, an aminated SFM-A, was achieved in the SAC-B producer (Pseudomonas fluorescens). These findings not only shed new insight on tetrahydroisoquinoline biosynthesis but also demonstrate the feasibility of engineering microorganisms to generate structurally more complex and biologically more active analogs by combinatorial biosynthesis.
ESTHER : Li_2008_J.Bacteriol_190_251
PubMedSearch : Li_2008_J.Bacteriol_190_251
PubMedID: 17981978

Title : Ameliorating effects of essential oil from Acori graminei rhizoma on learning and memory in aged rats and mice - Zhang_2007_J.Pharm.Pharmacol_59_301
Author(s) : Zhang H , Han T , Yu CH , Rahman K , Qin LP , Peng C
Ref : J Pharm Pharmacol , 59 :301 , 2007
Abstract : Although there are normal cognitive changes that take place as a person becomes older, ageing in humans is generally associated with a deterioration of cognitive performance, in particular of learning and memory. There are a number of herbal medicines that are reported to improve brain function and intelligence. In the present study, the ameliorating effects of an essential oil extracted from Acori graminei rhizoma on learning and memory in aged, dysmnesia rats and mice were determined using the step-down passive avoidance test and Y maze. Oral administration of the essential oil (0.02, 0.04 and 0.08 g kg(-1)) to rats for 30 days and to mice for 15 days improved the latency and number of errors in aged, dysmnesia rats and mice. The cerebral neurotransmitters in aged rats given the essential oil (0.02, 0.04, 0.08 g kg(-1)) for 30 days were also investigated, and increased levels of norepinephrine, dopamine and serotonin, and decreased levels of acetylcholinesterase activity were found. The results suggest that the essential oil improves cognitive function in aged animals possibly by increasing norepinephrine, dopamine and serotonin relative levels, and by decreasing the activity of acetylcholinesterase in the cerebra.
ESTHER : Zhang_2007_J.Pharm.Pharmacol_59_301
PubMedSearch : Zhang_2007_J.Pharm.Pharmacol_59_301
PubMedID: 17270083