Lee C

References (30)

Title : A Review of Recent Advances in the Management of Alzheimer's Disease - Thangwaritorn_2024_Cureus_16_e58416
Author(s) : Thangwaritorn S , Lee C , Metchikoff E , Razdan V , Ghafary S , Rivera D , Pinto A , Pemminati S
Ref : Cureus , 16 :e58416 , 2024
Abstract : Alzheimer's disease (AD) is the most common neurodegenerative condition and a form of dementia encountered in medical practice. Despite many proposed and attempted treatments, this disease remains a major puzzle in the public health systems worldwide. The initial part of this article provides an overview and illustration of the primary mechanisms responsible for neuronal damage in AD. Subsequently, it offers a critical evaluation of the most noteworthy studies on pharmacological therapy for AD and outlines recent advancements and novel approaches to managing this condition. Main properties, categorization, Food and Drug Administration (FDA) status, mechanisms of action, benefits, and common side effects of the classical and the most recently proposed pharmacological treatments for AD are described. The conventional pharmacological agents revised comprise cholinesterase inhibitors, monoclonal antibodies, and other therapies, such as memantine, valproic acid, and rosiglitazone. The innovative reviewed pharmacological agents comprise the monoclonal antibodies: donanemab, gantenerumab, solanezumab, bapineuzumab, crenezumab, and semorinemab. Nutritional supplements such as alpha-tocopherol (vitamin E) and caprylidene are also revised. Tau and amyloid-targeting treatments include methylthioninium moiety (MT), leuco-methylthioninium bis (LMTM), an oxidized form of MT, and tramiprosate, which inhibits the beta-amyloid (Abeta) monomer aggregation into toxic oligomers. Antidiabetic and anti-neuroinflammation drugs recently proposed for AD treatment are discussed. The antidiabetic drugs include NE3107, an anti-inflammatory and insulin sensitizer, and the diabetes mainstream drug metformin. The anti-neuroinflammatory AD therapies include the use of sodium oligomannate (GV-971), infusions with intravenous immunoglobulin aiming to decrease plasma levels of the constituents of Abeta plaques, and masitinib, a tyrosine kinase inhibitor that impacts mast and microglia cells. Additional anti-inflammatory agents being currently tested in phase-2 clinical trials, such as atomoxetine (selective norepinephrine reuptake inhibitor), losartan (angiotensin 2 receptor agonist), genistein (anti-inflammatory isoflavone neuroprotective agent), trans-resveratrol (polyphenol antioxidant plant estrogen), and benfotiamine (synthetic thiamine precursor), were reviewed. Lastly, drugs targeting Alzheimer's-associated symptoms, such as brexpiprazole (serotonin dopamine activity modulator) and suvorexant (orexin receptor antagonist), respectively, used for agitation and insomnia in AD patients, are reviewed. As experimental investigations and clinical research progress, there is a possibility that a combination of newly tested medications and traditional ones may emerge as a promising treatment option for AD in the future.
ESTHER : Thangwaritorn_2024_Cureus_16_e58416
PubMedSearch : Thangwaritorn_2024_Cureus_16_e58416
PubMedID: 38756263

Title : C-Terminal beta8-alpha9 Interaction Modulates Thermal Stability and Enzymatic Activity Differently in Hyperthermophilic Esterase EstE1 and Mesophilic Esterase rPPE - Nguyen_2023_Appl.Environ.Microbiol__e0066223
Author(s) : Nguyen TA , Jang SH , Lee C
Ref : Applied Environmental Microbiology , :e0066223 , 2023
Abstract : Hydrophobic interactions and hydrogen bonds are 2 types of noncovalent interactions that play distinct roles in the folding and structural stability of proteins. However, the specific roles of these interactions in hydrophobic or hydrophilic environments in alpha/beta-hydrolases are not fully understood. A hyperthermophilic esterase EstE1 in a dimer maintains the C-terminal beta8-alpha9 strand-helix via hydrophobic interactions (Phe276 and Leu299), constituting a closed dimer interface. Moreover, a mesophilic esterase rPPE in a monomer maintains the same strand-helix via a hydrogen bond (Tyr281 and Gln306). Unpaired polar residues (F276Y in EstE1 and Y281A/F and Q306A in rPPE) or reduced hydrophobic interactions (F276A/L299A in EstE1) between the beta8-alpha9 strand-helix decrease thermal stability. EstE1 (F276Y/L299Q) and rPPE WT, both with the beta8-alpha9 hydrogen bond, showed the same thermal stability as EstE1 WT and rPPE (Y281F/Q306L), which possess hydrophobic interactions instead. However, EstE1 (F276Y/L299Q) and rPPE WT exhibited higher enzymatic activity than EstE1 WT and rPPE (Y281F/Q306L), respectively. This suggests that alpha/beta-hydrolases favor the beta8-alpha9 hydrogen bond for catalytic activity in monomers or oligomers. Overall, these findings demonstrate how alpha/beta-hydrolases modulate hydrophobic interactions and hydrogen bonds to adapt to different environments. Both types of interactions contribute equally to thermal stability, but the hydrogen bond is preferred for catalytic activity. IMPORTANCE Esterases hydrolyze short to medium-chain monoesters and contain a catalytic His on a loop between the C-terminal beta8-strand and alpha9-helix. This study explores how hyperthermophilic esterase EstE1 and mesophilic esterase rPPE adapt to different temperatures by utilizing the beta8-alpha9 hydrogen bonds or hydrophobic interactions differently. EstE1 forms a hydrophobic dimer interface, while rPPE forms a monomer stabilized by a hydrogen bond. The study demonstrates that these enzymes stabilize beta8-alpha9 strand-helix differently but achieve similar thermal stability. While the beta8-alpha9 hydrogen bond or hydrophobic interactions contribute equally to thermal stability, the hydrogen bond provides higher activity due to increased catalytic His loop flexibility in both EstE1 and rPPE. These findings reveal how enzymes adapt to extreme environments while maintaining their functions and have implications for engineering enzymes with desired activities and stabilities.
ESTHER : Nguyen_2023_Appl.Environ.Microbiol__e0066223
PubMedSearch : Nguyen_2023_Appl.Environ.Microbiol__e0066223
PubMedID: 37289049
Gene_locus related to this paper: 9psed-l7pyq2 , 9arch-q5g935

Title : A chemical tool for blue light-inducible proximity photo-crosslinking in live cells - Mishra_2022_Chem.Sci_13_955
Author(s) : Mishra PK , Kang MG , Lee H , Kim S , Choi S , Sharma N , Park CM , Ko J , Lee C , Seo JK , Rhee HW
Ref : Chem Sci , 13 :955 , 2022
Abstract : We developed a proximity photo-crosslinking method (Spotlight) with a 4-azido-N-ethyl-1,8-naphthalimide (AzNP) moiety that can be converted to reactive aryl nitrene species using ambient blue light-emitting diode light. Using an AzNP-conjugated HaloTag ligand (VL1), blue light-induced photo-crosslinked products of various HaloTag-conjugated proteins of interest were detected in subcellular spaces in live cells. Chemical or heat stress-induced dynamic changes in the proteome were also detected, and photo-crosslinking in the mouse brain tissue was enabled. Using Spotlight, we further identified the host interactome of SARS-CoV-2 nucleocapsid (N) protein, which is essential for viral genome assembly. Mass analysis of the VL1-crosslinked product of N-HaloTag in HEK293T cells showed that RNA-binding proteins in stress granules were exclusively enriched in the cross-linked samples. These results tell that our method can reveal the interactome of protein of interest within a short distance in live cells.
ESTHER : Mishra_2022_Chem.Sci_13_955
PubMedSearch : Mishra_2022_Chem.Sci_13_955
Gene_locus related to this paper: rhoso-halo1

Title : CRISPR-Knockout of CSE Gene Improves Saccharification Efficiency by Reducing Lignin Content in Hybrid Poplar - Jang_2021_Int.J.Mol.Sci_22_
Author(s) : Jang HA , Bae EK , Kim MH , Park SJ , Choi NY , Pyo SW , Lee C , Jeong HY , Lee H , Choi YI , Ko JH
Ref : Int J Mol Sci , 22 : , 2021
Abstract : Caffeoyl shikimate esterase (CSE) has been shown to play an important role in lignin biosynthesis in plants and is, therefore, a promising target for generating improved lignocellulosic biomass crops for sustainable biofuel production. Populus spp. has two CSE genes (CSE1 and CSE2) and, thus, the hybrid poplar (Populus alba x P. glandulosa) investigated in this study has four CSE genes. Here, we present transgenic hybrid poplars with knockouts of each CSE gene achieved by CRISPR/Cas9. To knockout the CSE genes of the hybrid poplar, we designed three single guide RNAs (sg1-sg3), and produced three different transgenic poplars with either CSE1 (CSE1-sg2), CSE2 (CSE2-sg3), or both genes (CSE1/2-sg1) mutated. CSE1-sg2 and CSE2-sg3 poplars showed up to 29.1% reduction in lignin deposition with irregularly shaped xylem vessels. However, CSE1-sg2 and CSE2-sg3 poplars were morphologically indistinguishable from WT and showed no significant differences in growth in a long-term living modified organism (LMO) field-test covering four seasons. Gene expression analysis revealed that many lignin biosynthetic genes were downregulated in CSE1-sg2 and CSE2-sg3 poplars. Indeed, the CSE1-sg2 and CSE2-sg3 poplars had up to 25% higher saccharification efficiency than the WT control. Our results demonstrate that precise editing of CSE by CRISPR/Cas9 technology can improve lignocellulosic biomass without a growth penalty.
ESTHER : Jang_2021_Int.J.Mol.Sci_22_
PubMedSearch : Jang_2021_Int.J.Mol.Sci_22_
PubMedID: 34575913
Gene_locus related to this paper: arath-F14G24.3

Title : Chromenone Derivatives as Monoamine Oxidase Inhibitors from Marine-Derived MAR4 Clade Streptomyces sp. CNQ-031 - Oh_2021_J.Microbiol.Biotechnol__
Author(s) : Oh JM , Lee C , Nam SJ , Kim H
Ref : J Microbiol Biotechnol , : , 2021
Abstract : Three compounds were isolated from marine-derived Streptomyces sp. CNQ-031, and their inhibitory activities against monoamine oxidases (MAOs), acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and beta-secretase (BACE-1) were evaluated. Compound 1 (5,7-dihydroxy-2-isopropyl-4H-chromen-4-one) was a potent and selective inhibitor of MAO-A, with a 50% inhibitory concentration (IC(50)) of 2.70 microM and a selectivity index (SI) of 10.0 versus MAO-B. Compound 2 [5,7-dihydroxy-2-(1-methylpropyl)-4H-chromen-4-one] was a potent and low-selective inhibitor of MAO-B, with an IC(50) of 3.42 microM and an SI value of 2.02 versus MAO-A. Compound 3 (1-methoxyphenazine) did not inhibit MAO-A and MAO-B. All three compounds showed little inhibitory activity against AChE, BChE, and BACE-1. The K(i) value of compound 1 for MAO-A was 0.94 +/- 0.28 microM, and the K(i) values of compound 2 for MAO-A and MAO-B were 3.57 +/- 0.60 and 1.89 +/- 0.014 microM, respectively, with competitive inhibition. The 1-methylpropyl group in compound 2 increased the MAO-B inhibitory activity compared with the isopropyl group in compound 1. Inhibition of MAO-A and MAO-B by compounds 1 and 2 was recovered by dialysis experiments. These results suggest that compounds 1 and 2 are reversible, competitive inhibitors of MAOs and can be considered potential therapies for neurological disorders, such as depression and Alzheimer's disease.
ESTHER : Oh_2021_J.Microbiol.Biotechnol__
PubMedSearch : Oh_2021_J.Microbiol.Biotechnol__
PubMedID: 34099598

Title : Memory-enhancing effects of Ishige foliacea extract: In vitro and in vivo study - Kim_2020_J.Food.Biochem__e13162
Author(s) : Kim TE , Son HJ , Lim DW , Yoon M , Lee J , Kim YT , Han D , Lee C , Um MY
Ref : J Food Biochem , :e13162 , 2020
Abstract : Ishige foliacea is used as a functional food in East-Asian countries. We evaluated the memory-enhancing effect of an ethanol extract of I. foliacea (EEI) using in vitro and in vivo models. In vitro acetylcholinesterase and beta-secretase inhibitory activities, antioxidant properties, and neuroprotective effects against human neuronal cell death by H2 O2 and beta-amyloid (Abeta) were investigated. We explored the memory-enhancing effect and its underlying mechanism in a mouse model of scopolamine (SCO)-induced memory deficits. EEI showed free radical scavenging and acetylcholinesterase and beta-secretase inhibition activities. Additionally, EEI significantly decreased neuronal cell death induced by H2 O2 or Abeta in human neuroblastoma SH-SY5Y cells. In behavior tests, SCO-induced memory deficits was improved by EEI administration. EEI increased the protein expression of brain-derived neurotrophic factor (BDNF) and tropomyosin receptor kinase B (TrkB) and phosphorylated extracellular signal-regulated kinase, which are related to synaptic plasticity in the hippocampus. EEI may ameliorate memory deficits and prevent neurodegenerative disorders. PRACTICAL APPLICATIONS: As the population ages, dementia, a neurodegenerative disease, is becoming an important problem. Various Alzheimer's drugs have been developed based on the disease mechanism, but alternative treatments are required because of the low bioavailability and hepatotoxicity of current medications. Ishige foliacea is a type of brown algae containing various bioactive substances. Phlorotannins, known as brown algae polyphenols, have been studied for their various functionalities such as, anticancer, anti-obesity, antioxidant, and sleep improvement effects, and have attracted attention as raw materials for developing new natural products. We found that the EEI mitigates SCO-induced damage by protecting neurons from oxidative stress-induced cell damage, controlling synthesis mechanisms of the causative agents of AD, and activating BDNF-TrkB-ERK signaling to promote memory function in the hippocampus. The results of this study can serve as a foundation for further research. Additionally, I. foliacea may be useful for treating and improving AD.
ESTHER : Kim_2020_J.Food.Biochem__e13162
PubMedSearch : Kim_2020_J.Food.Biochem__e13162
PubMedID: 32020642

Title : Makes caterpillars floppy-like effector-containing MARTX toxins require host ADP-ribosylation factor (ARF) proteins for systemic pathogenicity - Lee_2019_Proc.Natl.Acad.Sci.U.S.A_116_18031
Author(s) : Lee Y , Kim BS , Choi S , Lee EY , Park S , Hwang J , Kwon Y , Hyun J , Lee C , Kim JF , Eom SH , Kim MH
Ref : Proc Natl Acad Sci U S A , 116 :18031 , 2019
Abstract : Upon invading target cells, multifunctional autoprocessing repeats-in-toxin (MARTX) toxins secreted by bacterial pathogens release their disease-related modularly structured effector domains. However, it is unclear how a diverse repertoire of effector domains within these toxins are processed and activated. Here, we report that Makes caterpillars floppy-like effector (MCF)-containing MARTX toxins require ubiquitous ADP-ribosylation factor (ARF) proteins for processing and activation of intermediate effector modules, which localize in different subcellular compartments following limited processing of holo effector modules by the internal cysteine protease. Effector domains structured tandemly with MCF in intermediate modules become disengaged and fully activated by MCF, which aggressively interacts with ARF proteins present at the same location as intermediate modules and is converted allosterically into a catalytically competent protease. MCF-mediated effector processing leads ultimately to severe virulence in mice via an MCF-mediated ARF switching mechanism across subcellular compartments. This work provides insight into how bacteria take advantage of host systems to induce systemic pathogenicity.
ESTHER : Lee_2019_Proc.Natl.Acad.Sci.U.S.A_116_18031
PubMedSearch : Lee_2019_Proc.Natl.Acad.Sci.U.S.A_116_18031
PubMedID: 31427506
Gene_locus related to this paper: vibvy-q7mdk6

Title : Newly developed reversible MAO-B inhibitor circumvents the shortcomings of irreversible inhibitors in Alzheimer's disease - Park_2019_Sci.Adv_5_eaav0316
Author(s) : Park JH , Ju YH , Choi JW , Song HJ , Jang BK , Woo J , Chun H , Kim HJ , Shin SJ , Yarishkin O , Jo S , Park M , Yeon SK , Kim S , Kim J , Nam MH , Londhe AM , Cho SJ , Cho S , Lee C , Hwang SY , Kim SW , Oh SJ , Cho J , Pae AN , Lee CJ , Park KD
Ref : Sci Adv , 5 :eaav0316 , 2019
Abstract : Monoamine oxidase-B (MAO-B) has recently emerged as a potential therapeutic target for Alzheimer's disease (AD) because of its association with aberrant gamma-aminobutyric acid (GABA) production in reactive astrocytes. Although short-term treatment with irreversible MAO-B inhibitors, such as selegiline, improves cognitive deficits in AD patients, long-term treatments have shown disappointing results. We show that prolonged treatment with selegiline fails to reduce aberrant astrocytic GABA levels and rescue memory impairment in APP/PS1 mice, an animal model of AD, because of increased activity in compensatory genes for a GABA-synthesizing enzyme, diamine oxidase (DAO). We have developed a potent, highly selective, and reversible MAO-B inhibitor, KDS2010 (IC(50) = 7.6 nM; 12,500-fold selectivity over MAO-A), which overcomes the disadvantages of the irreversible MAO-B inhibitor. Long-term treatment with KDS2010 does not induce compensatory mechanisms, thereby significantly attenuating increased astrocytic GABA levels and astrogliosis, enhancing synaptic transmission, and rescuing learning and memory impairments in APP/PS1 mice.
ESTHER : Park_2019_Sci.Adv_5_eaav0316
PubMedSearch : Park_2019_Sci.Adv_5_eaav0316
PubMedID: 30906861

Title : Distinct roles of an ionic interaction holding an alpha-helix with catalytic Asp and a beta-strand with catalytic His in a hyperthermophilic esterase EstE1 and a mesophilic esterase rPPE - Dachuri_2019_Extremophiles_23_649
Author(s) : Dachuri V , Truongvan N , DangThu Q , Jang SH , Lee C
Ref : Extremophiles , 23 :649 , 2019
Abstract : An ionic interaction that holds an alpha-helix and a beta-strand on which catalytic Asp and His residues are located, respectively, is conserved in a hyperthermophilic esterase EstE1 (optimum temperature 70 degreesC) and a mesophilic esterase rPPE (optimum temperature 50 degreesC). We investigated the role of an ionic interaction between E258 and R275 in EstE1 and that between E263 and R280 in rPPE in active-site stability of serine esterases adapted to different temperatures. Ala substitutions caused a 5-10 degreesC decrease in the optimum temperature of both EstE1 and rPPE mutants. Surprisingly, disruption of the ionic interaction caused larger effects on the conformational flexibility of EstE1 mutants despite their rigid structures, whereas the disruption had fewer effects on the thermal stability of EstE1 mutants at 60-70 degreesC, as the structure of EstE1 was adapted to high temperatures. In contrast, mesophilic rPPE mutants showed dramatic decreases in thermal stability at 40-50 degreesC, but less changes in conformational flexibility because of their inherently flexible structures. The results of this study suggest that the ionic interaction between the alpha-helix with catalytic Asp and the beta-strand with catalytic His plays an important role in the active-site conformation of EstE1 and rPPE, with larger effects on the conformational flexibility of hyperthermophilic EstE1 and the thermal stability of mesophilic rPPE.
ESTHER : Dachuri_2019_Extremophiles_23_649
PubMedSearch : Dachuri_2019_Extremophiles_23_649
PubMedID: 31332517
Gene_locus related to this paper: 9psed-l7pyq2

Title : Structure-guided synthesis of a protein-based fluorescent sensor for alkyl halides - Kang_2017_Chem.Commun.(Camb)_53_9226
Author(s) : Kang MG , Lee H , Kim BH , Dunbayev Y , Seo JK , Lee C , Rhee HW
Ref : Chem Commun (Camb) , 53 :9226 , 2017
Abstract : Alkyl halides are potentially mutagenic carcinogens. However, no efficient fluorescent sensor for alkyl halide detection in human-derived samples has been developed to date. Herein, we report a new protein-based fluorescent sensor for alkyl halides. Analysis of the HaloTag holo-crystal structure with its covalently attached ligand revealed an unexpected cavity, allowing for the design of a new fluorogenic ligand. This ligand showed the highest fluorescence response (300-fold) and fastest binding kinetics (t1/2 < 150 s) to a HaloTag mutant (M175P) protein. This protein-based sensor system was effectively used to detect alkyl halides in human serum and monitor real-time protein alkylation.
ESTHER : Kang_2017_Chem.Commun.(Camb)_53_9226
PubMedSearch : Kang_2017_Chem.Commun.(Camb)_53_9226
PubMedID: 28766590
Gene_locus related to this paper: rhoso-halo1

Title : Conserved tyrosine 182 residue in hyperthermophilic esterase EstE1 plays a critical role in stabilizing the active site - Truongvan_2016_Extremophiles_20_187
Author(s) : Truongvan N , Chung HS , Jang SH , Lee C
Ref : Extremophiles , 20 :187 , 2016
Abstract : An aromatic amino acid, Tyr or Trp, located in the esterase active site wall, is highly conserved, with hyperthermophilic esterases showing preference for Tyr and lower temperature esterases showing preference for Trp. In this study, we investigated the role of Tyr(182) in the active site wall of hyperthermophilic esterase EstE1. Mutation of Tyr to Phe or Ala had a moderate effect on EstE1 thermal stability. However, a small-to-large mutation such as Tyr to His or Trp had a devastating effect on thermal stability. All mutant EstE1 enzymes showed reduced catalytic rates and enhanced substrate affinities as compared with wild-type EstE1. Hydrogen bond formation involving Tyr(182) was unimportant for maintaining EstE1 thermal stability, as the EstE1 structure is already adapted to high temperatures via increased intramolecular interactions. However, removal of hydrogen bond from Tyr(182) significantly decreased EstE1 catalytic activity, suggesting its role in stabilization of the active site. These results suggest that Tyr is preferred over a similarly sized Phe residue or bulky His or Trp residue in the active site walls of hyperthermophilic esterases for stabilizing the active site and regulating catalytic activity at high temperatures.
ESTHER : Truongvan_2016_Extremophiles_20_187
PubMedSearch : Truongvan_2016_Extremophiles_20_187
PubMedID: 26838013

Title : Flexibility and Stability Trade-Off in Active Site of Cold-Adapted Pseudomonas mandelii Esterase EstK - Truongvanvan_2016_Biochemistry_55_3542
Author(s) : Truongvan N , Jang SH , Lee C
Ref : Biochemistry , 55 :3542 , 2016
Abstract : Cold-adapted enzymes exhibit enhanced conformational flexibility, especially in their active sites, as compared with their warmer-temperature counterparts. However, the mechanism by which cold-adapted enzymes maintain their active site stability is largely unknown. In this study, we investigated the role of conserved D308-Y309 residues located in the same loop as the catalytic H307 residue in the cold-adapted esterase EstK from Pseudomonas mandelii. Mutation of D308 and/or Y309 to Ala or deletion resulted in increased conformational flexibility. Particularly, the D308A or Y309A mutant showed enhanced substrate affinity and catalytic rate, as compared with wild-type EstK, via enlargement of the active site. However, all mutant EstK enzymes exhibited reduced thermal stability. The effect of mutation was greater for D308 than Y309. These results indicate that D308 is not preferable for substrate selection and catalytic activity, whereas hydrogen bond formation involving D308 is critical for active site stabilization. Taken together, conformation of the EstK active site is constrained via flexibility-stability trade-off for enzyme catalysis and thermal stability. Our study provides further insights into active site stabilization of cold-adapted enzymes.
ESTHER : Truongvanvan_2016_Biochemistry_55_3542
PubMedSearch : Truongvanvan_2016_Biochemistry_55_3542
PubMedID: 27259687
Gene_locus related to this paper: 9arch-q5g935

Title : Enhanced catalytic site thermal stability of cold-adapted esterase EstK by a W208Y mutation - Boyineni_2014_Biochim.Biophys.Acta_1844_1076
Author(s) : Boyineni J , Kim J , Kang BS , Lee C , Jang SH
Ref : Biochimica & Biophysica Acta , 1844 :1076 , 2014
Abstract : Hydrophobic interactions are known to play an important role for cold-adaptation of proteins; however, the role of amino acid residue, Trp, has not been systematically investigated. The extracellular esterase, EstK, which was isolated from the cold-adapted bacterium Pseudomonas mandelii, has 5 Trp residues. In this study, the effects of Trp mutation on thermal stability, catalytic activity, and conformational change of EstK were investigated. Among the 5 Trp residues, W(208) was the most crucial in maintaining structural conformation and thermal stability of the enzyme. Surprisingly, mutation of W(208) to Tyr (W(208)Y) showed an increased catalytic site thermal stability at ambient temperatures with a 13-fold increase in the activity at 40 degrees C compared to wild-type EstK. The structure model of W(208)Y suggested that Y(208) could form a hydrogen bond with D(308), which is located next to catalytic residue H(307), stabilizing the catalytic domain. Interestingly, Tyr was conserved in the corresponding position of hyper-thermophilic esterases EstE1 and AFEST, which are active at high temperatures. Our study provides a novel insight into the engineering of the catalytic site of cold-adapted enzymes with increased thermal stability and catalytic activity at ambient temperatures.
ESTHER : Boyineni_2014_Biochim.Biophys.Acta_1844_1076
PubMedSearch : Boyineni_2014_Biochim.Biophys.Acta_1844_1076
PubMedID: 24667115
Gene_locus related to this paper: 9psed-h6vxl7

Title : Draft Genome Sequence of Pseudomonas aeruginosa SG17M, an Environmental Isolate Belonging to Clone C, Prevalent in Patients and Aquatic Habitats - Lee_2014_Genome.Announc_2_e00186
Author(s) : Lee C , Peters V , Melefors O , Romling U
Ref : Genome Announc , 2 :e00186 , 2014
Abstract : Pseudomonas aeruginosa SG17M is an environmental isolate recovered from river water in the city of Mulheim, Germany. SG17M belongs to clone C, which is distributed worldwide. This is the first clone C strain whose genome sequence has been determined.
ESTHER : Lee_2014_Genome.Announc_2_e00186
PubMedSearch : Lee_2014_Genome.Announc_2_e00186
PubMedID: 24652978
Gene_locus related to this paper: pseae-q9i252

Title : IL-6 attenuates trimethyltin-induced cognitive dysfunction via activation of JAK2\/STAT3, M1 mAChR and ERK signaling network - Kim_2013_Cell.Signal_25_1348
Author(s) : Kim BK , Tran HY , Shin EJ , Lee C , Chung YH , Jeong JH , Bach JH , Kim WK , Park DH , Saito K , Nabeshima T , Kim HC
Ref : Cell Signal , 25 :1348 , 2013
Abstract : We previously reported that interleukin (IL)-6 deficiency potentiates trimethyltin (TMT)-induced convulsive neurotoxicity. The purpose in this study was to investigate the molecular mechanism by which cytokines affect TMT-induced cognitive impairment. To accomplish this, we examined hippocampal changes in Janus kinase 2 (JAK2)/signal transducer and activator of transcription 3 (STAT3) signaling in relation to cholinergic parameters after TMT treatment in mice genetically deficient in IL-6 (IL-6(-/-)), tumor necrosis factor-alpha (TNF-alpha(-/-)), or interferon-gamma (IFN-gamma(-/-)). The IL-6(-/-) mice were the most susceptible to TMT-induced cognitive dysfunction and exhibited significant decreases in JAK2/STAT3 signaling and M1 muscarinic acetylcholine receptor (mAChR) expression, as well as other cholinergic parameters, compared with wild-type (WT) animals. Recombinant IL-6 protein (rIL-6) significantly attenuated these impairments in TMT-treated IL-6(-/-) mice, whereas an IL-6 receptor antibody potentiated these impairments in TMT-treated WT animals. Inhibition of JAK2 with AG490 or inhibition of cholinergic signaling with the M1 mAChR antagonist dicyclomine counteracted the attenuating effects of rIL-6 on phosphorylated extracellular signal-regulated kinase (ERK) expression, or on cognitive impairment in TMT-treated IL-6(-/-) mice. However, neither AG490 nor dicyclomine significantly attenuated effects of rIL-6 on acetylcholinesterase values. Our results suggest that activation of JAK2/STAT3 signaling and upregulation of the M1 mAChR are essential components of IL-6-mediated memory improvement against TMT toxicity.
ESTHER : Kim_2013_Cell.Signal_25_1348
PubMedSearch : Kim_2013_Cell.Signal_25_1348
PubMedID: 23499905

Title : Association of LIPC and advanced age-related macular degeneration - Lee_2013_Eye.(Lond)_27_265
Author(s) : Lee J , Zeng J , Hughes G , Chen Y , Grob S , Zhao L , Lee C , Krupa M , Quach J , Luo J , Wei X , Zhang X , Zhu J , Duan Y , Ferreyra H , Goldbaum M , Haw W , Shaw PX , Tang L , Zhang K
Ref : Eye (Lond) , 27 :265 , 2013
Abstract : PURPOSE: To determine whether there is an association between hepatic lipase (LIPC) and age-related macular degeneration (AMD) in two independent Caucasian cohorts.
METHODS: A discovery cohort of 1626 patients with advanced AMD and 859 normal controls and a replication cohort of 2159 cases and 1150 controls were genotyped for two single-nucleotide polymorphisms (SNPs) in the promoter region of LIPC. The associations between the SNPs and AMD were examined by chi(2) tests.
RESULTS: In the discovery cohort, rs493258 and rs10468017 were both associated with advanced AMD (P=9.63E-3 and P=0.048, respectively). The association was corroborated in the replication cohort (P=4.48E-03 for rs493258 and P=0.015 for rs10468017). Combined analysis resulted in even more significant associations (P=1.21E-04 for rs493258 and P=1.67E-03 for rs10468017). CONCLUSION: The LIPC promoter variants rs493258 and rs10468017 were associated with advanced AMD in two independent Caucasian populations, confirming that LIPC polymorphisms may be a genetic risk factor for AMD in the Caucasian population.
ESTHER : Lee_2013_Eye.(Lond)_27_265
PubMedSearch : Lee_2013_Eye.(Lond)_27_265
PubMedID: 23348725

Title : An Organic Solvent-Tolerant Alkaline Lipase from Cold-Adapted Pseudomonas mandelii: Cloning, Expression, and Characterization - Kim_2013_Biosci.Biotechnol.Biochem_77_320
Author(s) : Kim J , Jang SH , Lee C
Ref : Biosci Biotechnol Biochem , 77 :320 , 2013
Abstract : A gene encoding a novel organic solvent-tolerant alkaline lipase, lipS (GenBank ID JQ071496), was cloned from cold-adapted Pseudomonas mandelii. Recombinant LipS was expressed in Escherichia coli as a 32-kDa soluble protein and was purified by standard procedures. It maintained more than 80% of its activity under alkaline conditions, pH 8-10.5, with an apparent optimum temperature range of 40-50 degrees C. It maintained thermal stability from 4 to 50 degrees C. After 1 h of incubation at 60 degrees C, approximately 50% of its activity remained. It retained its activity in organic solvents, and activity increased in the presence of ethanol and of DMSO. Our data indicate that LipS is an alkaline lipase with relatively high thermal stability and notable tolerance of organic solvents.
ESTHER : Kim_2013_Biosci.Biotechnol.Biochem_77_320
PubMedSearch : Kim_2013_Biosci.Biotechnol.Biochem_77_320
PubMedID: 23391923
Gene_locus related to this paper: 9psed-h2etp9

Title : Cloning, expression, and characterization of a recombinant esterase from cold-adapted Pseudomonas mandelii - Lee_2013_Appl.Biochem.Biotechnol_169_29
Author(s) : Lee C , Kim J , Hong S , Goo B , Lee S , Jang SH
Ref : Appl Biochem Biotechnol , 169 :29 , 2013
Abstract : A gene coding for the extracellular esterase (EstK) was cloned from the psychrotrophic bacterium Pseudomonas mandelii based on its partial amino acid sequence as determined by mass spectrometry. The entire open reading frame consisting of 1,011 bp was expressed in Escherichia coli as a soluble protein and purified by nickel-chelated affinity chromatography and Capto Q column chromatography. Here, we show that the 33-kDa recombinant EstK protein (rEstKsp) had a substrate preference for esters of short-chain fatty acids, especially, p-nitrophenyl acetate. Optimum activity of rEstKsp was at pH 8.5 and 40 degrees C. The esterase activity remained similar from a range of 4 - 20 degrees C, but the maximum activity varied depending upon pH. With p-nitrophenyl acetate as the substrate, K (M) was 210 muM and k (cat) was 3.4 s(-1). Circular dichroism and fluorescence spectroscopy results revealed that rEstKsp had a predominantly alpha-helical structure and maintained its folded state at 4 approximately 40 degrees C. Interestingly, the tertiary structure of rEstKsp was predicted based on the structures of other hyperthermophilic esterases. Our results demonstrated that both native and rEstKsp are active at low temperatures and have a unique substrate preference for p-nitrophenyl acetate.
ESTHER : Lee_2013_Appl.Biochem.Biotechnol_169_29
PubMedSearch : Lee_2013_Appl.Biochem.Biotechnol_169_29
PubMedID: 23117417
Gene_locus related to this paper: 9psed-h6vxl7

Title : The zebrafish reference genome sequence and its relationship to the human genome - Howe_2013_Nature_496_498
Author(s) : Howe K , Clark MD , Torroja CF , Torrance J , Berthelot C , Muffato M , Collins JE , Humphray S , McLaren K , Matthews L , Mclaren S , Sealy I , Caccamo M , Churcher C , Scott C , Barrett JC , Koch R , Rauch GJ , White S , Chow W , Kilian B , Quintais LT , Guerra-Assuncao JA , Zhou Y , Gu Y , Yen J , Vogel JH , Eyre T , Redmond S , Banerjee R , Chi J , Fu B , Langley E , Maguire SF , Laird GK , Lloyd D , Kenyon E , Donaldson S , Sehra H , Almeida-King J , Loveland J , Trevanion S , Jones M , Quail M , Willey D , Hunt A , Burton J , Sims S , McLay K , Plumb B , Davis J , Clee C , Oliver K , Clark R , Riddle C , Elliot D , Threadgold G , Harden G , Ware D , Begum S , Mortimore B , Kerry G , Heath P , Phillimore B , Tracey A , Corby N , Dunn M , Johnson C , Wood J , Clark S , Pelan S , Griffiths G , Smith M , Glithero R , Howden P , Barker N , Lloyd C , Stevens C , Harley J , Holt K , Panagiotidis G , Lovell J , Beasley H , Henderson C , Gordon D , Auger K , Wright D , Collins J , Raisen C , Dyer L , Leung K , Robertson L , Ambridge K , Leongamornlert D , McGuire S , Gilderthorp R , Griffiths C , Manthravadi D , Nichol S , Barker G , Whitehead S , Kay M , Brown J , Murnane C , Gray E , Humphries M , Sycamore N , Barker D , Saunders D , Wallis J , Babbage A , Hammond S , Mashreghi-Mohammadi M , Barr L , Martin S , Wray P , Ellington A , Matthews N , Ellwood M , Woodmansey R , Clark G , Cooper J , Tromans A , Grafham D , Skuce C , Pandian R , Andrews R , Harrison E , Kimberley A , Garnett J , Fosker N , Hall R , Garner P , Kelly D , Bird C , Palmer S , Gehring I , Berger A , Dooley CM , Ersan-Urun Z , Eser C , Geiger H , Geisler M , Karotki L , Kirn A , Konantz J , Konantz M , Oberlander M , Rudolph-Geiger S , Teucke M , Lanz C , Raddatz G , Osoegawa K , Zhu B , Rapp A , Widaa S , Langford C , Yang F , Schuster SC , Carter NP , Harrow J , Ning Z , Herrero J , Searle SM , Enright A , Geisler R , Plasterk RH , Lee C , Westerfield M , de Jong PJ , Zon LI , Postlethwait JH , Nusslein-Volhard C , Hubbard TJ , Roest Crollius H , Rogers J , Stemple DL
Ref : Nature , 496 :498 , 2013
Abstract : Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.
ESTHER : Howe_2013_Nature_496_498
PubMedSearch : Howe_2013_Nature_496_498
PubMedID: 23594743
Gene_locus related to this paper: danre-1neur , danre-ABHD10b , danre-a9jrf7 , danre-d2x2g3 , danre-e7ezq9 , danre-e7ff77 , danre-ndr3 , danre-nlgn4a , danre-q1mti5 , danre-q6nyz4 , danre-q6p2u2 , danre-q7t359 , danre-q08c93 , danre-A2BGU9 , danre-f1q676 , danre-e7f0z8 , danre-e7ez27 , danre-e7f2w1 , danre-f1qid7 , danre-a0a0g2kru2 , danre-f1qla7 , danre-a9jr90 , danre-e7f070 , danre-f172a , danre-e7fb35 , danre-a7mbu9 , danre-f1qtr2

Title : A new pancreatic lipase inhibitor from Broussonetia kanzinoki - Ahn_2012_Bioorg.Med.Chem.Lett_22_2760
Author(s) : Ahn JH , Liu Q , Lee C , Ahn MJ , Yoo HS , Hwang BY , Lee MK
Ref : Bioorganic & Medicinal Chemistry Lett , 22 :2760 , 2012
Abstract : A new phenolic compound, broussonone A (1) were isolated from the stem barks of Broussonetia kanzinoki (Moraceae), together with two diphenylpropanes, broussonin A (2), broussonin B (3), two flavans, 7,4'-dihydroxyflavan (4), 3',7-dihydroxy-4'-methoxyflavan (5), and two flavones, 3,7-dihydroxy-4'-methoxyflavone (6), 3,7,3'-trihydroxy-4'-methoxyflavone (7). Compound 1 showed noncompetitive inhibitory activity on pancreatic lipase with an IC(50) of 28.4 muM. In addition, compounds 1-5 significantly inhibited adipocyte differentiation in 3T3-L1 cells as measured fat accumulation using Oil Red O assay.
ESTHER : Ahn_2012_Bioorg.Med.Chem.Lett_22_2760
PubMedSearch : Ahn_2012_Bioorg.Med.Chem.Lett_22_2760
PubMedID: 22450131

Title : Genome sequence of cold-adapted Pseudomonas mandelii strain JR-1 - Jang_2012_J.Bacteriol_194_3263
Author(s) : Jang SH , Kim J , Hong S , Lee C
Ref : Journal of Bacteriology , 194 :3263 , 2012
Abstract : Pseudomonas mandelii is a cold-adapted bacterium that can grow at 4 degrees C but not at 37 degrees C. Here we report the draft genome sequence of P. mandelii strain JR-1.
ESTHER : Jang_2012_J.Bacteriol_194_3263
PubMedSearch : Jang_2012_J.Bacteriol_194_3263
PubMedID: 22628497
Gene_locus related to this paper: 9psed-w6ve15 , 9psed-a0a024ebb1 , 9psed-a0a024e9h9

Title : Purification and properties of an extracellular esterase from a cold-adapted Pseudomonas mandelii - Hong_2012_Biotechnol.Lett_34_1051
Author(s) : Hong S , Lee C , Jang SH
Ref : Biotechnol Lett , 34 :1051 , 2012
Abstract : An extracellular esterase, EstK, was purified from the psychrotrophic bacterium Pseudomonas mandelii grown at 25 degreesC. Prior to harvest, cells were treated with 0.2 M MgCl2 to precipitate lipopolysaccharides in the outer membranes, which otherwise form aggregates with the secreted enzymes. EstK was purified to homogeneity using standard procedures. It had substrate specificity towards esters of short-chain fatty acids, particularly, p-nitrophenyl acetate. Optimum activity of EstK was at 40 degreesC; at 4 degreesC the activity was ~50% of its maximum. EstK has a unique substrate preference for p-nitrophenyl acetate and remains active at low temperatures.
ESTHER : Hong_2012_Biotechnol.Lett_34_1051
PubMedSearch : Hong_2012_Biotechnol.Lett_34_1051
PubMedID: 22315100
Gene_locus related to this paper: 9psed-h6vxl7

Title : PKA-activated ApAF-ApC\/EBP heterodimer is a key downstream effector of ApCREB and is necessary and sufficient for the consolidation of long-term facilitation - Lee_2006_J.Cell.Biol_174_827
Author(s) : Lee JA , Lee SH , Lee C , Chang DJ , Lee Y , Kim H , Cheang YH , Ko HG , Lee YS , Jun H , Bartsch D , Kandel ER , Kaang BK
Ref : Journal of Cell Biology , 174 :827 , 2006
Abstract : Long-term memory requires transcriptional regulation by a combination of positive and negative transcription factors. Aplysia activating factor (ApAF) is known to be a positive transcription factor that forms heterodimers with ApC/EBP and ApCREB2. How these heterodimers are regulated and how they participate in the consolidation of long-term facilitation (LTF) has not, however, been characterized. We found that the functional activation of ApAF required phosphorylation of ApAF by PKA on Ser-266. In addition, ApAF lowered the threshold of LTF by forming a heterodimer with ApCREB2. Moreover, once activated by PKA, the ApAF-ApC/EBP heterodimer transactivates enhancer response element-containing genes and can induce LTF in the absence of CRE- and CREB-mediated gene expression. Collectively, these results suggest that PKA-activated ApAF-ApC/EBP heterodimer is a core downstream effector of ApCREB in the consolidation of LTF.
ESTHER : Lee_2006_J.Cell.Biol_174_827
PubMedSearch : Lee_2006_J.Cell.Biol_174_827
PubMedID: 16966424

Title : Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain - Gill_2005_J.Bacteriol_187_2426
Author(s) : Gill SR , Fouts DE , Archer GL , Mongodin EF , DeBoy RT , Ravel J , Paulsen IT , Kolonay JF , Brinkac L , Beanan M , Dodson RJ , Daugherty SC , Madupu R , Angiuoli SV , Durkin AS , Haft DH , Vamathevan J , Khouri H , Utterback T , Lee C , Dimitrov G , Jiang L , Qin H , Weidman J , Tran K , Kang K , Hance IR , Nelson KE , Fraser CM
Ref : Journal of Bacteriology , 187 :2426 , 2005
Abstract : Staphylococcus aureus is an opportunistic pathogen and the major causative agent of numerous hospital- and community-acquired infections. Staphylococcus epidermidis has emerged as a causative agent of infections often associated with implanted medical devices. We have sequenced the approximately 2.8-Mb genome of S. aureus COL, an early methicillin-resistant isolate, and the approximately 2.6-Mb genome of S. epidermidis RP62a, a methicillin-resistant biofilm isolate. Comparative analysis of these and other staphylococcal genomes was used to explore the evolution of virulence and resistance between these two species. The S. aureus and S. epidermidis genomes are syntenic throughout their lengths and share a core set of 1,681 open reading frames. Genome islands in nonsyntenic regions are the primary source of variations in pathogenicity and resistance. Gene transfer between staphylococci and low-GC-content gram-positive bacteria appears to have shaped their virulence and resistance profiles. Integrated plasmids in S. epidermidis carry genes encoding resistance to cadmium and species-specific LPXTG surface proteins. A novel genome island encodes multiple phenol-soluble modulins, a potential S. epidermidis virulence factor. S. epidermidis contains the cap operon, encoding the polyglutamate capsule, a major virulence factor in Bacillus anthracis. Additional phenotypic differences are likely the result of single nucleotide polymorphisms, which are most numerous in cell envelope proteins. Overall differences in pathogenicity can be attributed to genome islands in S. aureus which encode enterotoxins, exotoxins, leukocidins, and leukotoxins not found in S. epidermidis.
ESTHER : Gill_2005_J.Bacteriol_187_2426
PubMedSearch : Gill_2005_J.Bacteriol_187_2426
PubMedID: 15774886
Gene_locus related to this paper: staau-LIP , staau-lipas , staau-MW0741 , staau-MW2456 , staau-q6gfm6 , staau-SA0011 , staau-SA0569 , staau-SA0572 , staau-SA0897 , staau-SA1143 , staau-SA2240 , staau-SA2306 , staau-SA2367 , staau-SA2422 , staau-SAV0321 , staau-SAV0446 , staau-SAV0457 , staau-SAV0655 , staau-SAV1014 , staau-SAV1765 , staau-SAV1793 , staau-SAV2188 , staau-SAV2350 , staau-SAV2484 , staau-SAV2594 , staep-lipas , staep-SE0011 , staep-SE0226 , staep-SE0386 , staep-SE0389 , staep-SE0424 , staep-SE0564 , staep-SE0714 , staep-SE0745 , staep-SE0980 , staep-SE1436 , staep-SE1460 , staep-SE1510 , staep-SE1780 , staep-SE1929 , staep-SERP2035 , staep-SE2050 , staep-SE2095 , staep-SE2213 , staep-SE2328

Title : Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent - Jeong_2005_Nucleic.Acids.Res_33_7066
Author(s) : Jeong H , Yim JH , Lee C , Choi SH , Park YK , Yoon SH , Hur CG , Kang HY , Kim D , Lee HH , Park KH , Park SH , Park HS , Lee HK , Oh TK , Kim JF
Ref : Nucleic Acids Research , 33 :7066 , 2005
Abstract : Harmful algal blooms, caused by rapid growth and accumulation of certain microalgae in the ocean, pose considerable impacts on marine environments, aquatic industries and even public health. Here, we present the 7.2-megabase genome of the marine bacterium Hahella chejuensis including genes responsible for the biosynthesis of a pigment which has the lytic activity against a red-tide dinoflagellate. H.chejuensis is the first sequenced species in the Oceanospiralles clade, and sequence analysis revealed its distant relationship to the Pseudomonas group. The genome was well equipped with genes for basic metabolic capabilities and contained a large number of genes involved in regulation or transport as well as with characteristics as a marine heterotroph. Sequence analysis also revealed a multitude of genes of functional equivalence or of possible foreign origin. Functions encoded in the genomic islands include biosynthesis of exopolysacchrides, toxins, polyketides or non-ribosomal peptides, iron utilization, motility, type III protein secretion and pigmentation. Molecular structure of the algicidal pigment, which was determined through LC-ESI-MS/MS and NMR analyses, indicated that it is prodigiosin. In conclusion, our work provides new insights into mitigating algal blooms in addition to genetic make-up, physiology, biotic interactions and biological roles in the community of a marine bacterium.
ESTHER : Jeong_2005_Nucleic.Acids.Res_33_7066
PubMedSearch : Jeong_2005_Nucleic.Acids.Res_33_7066
PubMedID: 16352867
Gene_locus related to this paper: hahch-q2s6v8 , hahch-q2s7u4 , hahch-q2s8m0 , hahch-q2s9b5 , hahch-q2s9n3 , hahch-q2s796 , hahch-q2s803 , hahch-q2s809 , hahch-q2s829 , hahch-q2sae5 , hahch-q2sav4 , hahch-q2sbd6 , hahch-q2sc65 , hahch-q2scc5 , hahch-q2sci6 , hahch-q2sct6 , hahch-q2scw7 , hahch-q2sdy2 , hahch-q2seh8 , hahch-q2seq6 , hahch-q2sfm2 , hahch-q2sfm4 , hahch-q2sfm9 , hahch-q2sfx3 , hahch-q2sgj4 , hahch-q2sgn6 , hahch-q2sgt0 , hahch-q2sgz8 , hahch-q2shj8 , hahch-q2shp0 , hahch-q2shq5 , hahch-q2shv0 , hahch-q2shv4 , hahch-q2shz6 , hahch-q2sic0 , hahch-q2sil6 , hahch-q2sj56 , hahch-q2sje1 , hahch-q2sje8 , hahch-q2skf9 , hahch-q2skg3 , hahch-q2skl5 , hahch-q2skv5 , hahch-q2sl80 , hahch-q2sll2 , hahch-q2slq4 , hahch-q2sls7 , hahch-q2sm17 , hahch-q2sn09 , hahch-q2sn54 , hahch-q2snn5 , hahch-q2snq6 , hahch-q2snw9 , hahch-q2spi5 , hahch-q2spk1 , hahch-q2spm8 , hahch-q2sq02 , hahch-q2sqg8 , hahch-q2sqn4 , hahch-q2sqx6 , hahch-q2sjs2

Title : Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis - Heidelberg_2002_Nat.Biotechnol_20_1118
Author(s) : Heidelberg JF , Paulsen IT , Nelson KE , Gaidos EJ , Nelson WC , Read TD , Eisen JA , Seshadri R , Ward N , Methe B , Clayton RA , Meyer T , Tsapin A , Scott J , Beanan M , Brinkac L , Daugherty S , DeBoy RT , Dodson RJ , Durkin AS , Haft DH , Kolonay JF , Madupu R , Peterson JD , Umayam LA , White O , Wolf AM , Vamathevan J , Weidman J , Impraim M , Lee K , Berry K , Lee C , Mueller J , Khouri H , Gill J , Utterback TR , McDonald LA , Feldblyum TV , Smith HO , Venter JC , Nealson KH , Fraser CM
Ref : Nat Biotechnol , 20 :1118 , 2002
Abstract : Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities, conferred in part by multicomponent, branched electron transport systems. Here we report the sequencing of the S. oneidensis genome, which consists of a 4,969,803-base pair circular chromosome with 4,758 predicted protein-encoding open reading frames (CDS) and a 161,613-base pair plasmid with 173 CDSs. We identified the first Shewanella lambda-like phage, providing a potential tool for further genome engineering. Genome analysis revealed 39 c-type cytochromes, including 32 previously unidentified in S. oneidensis, and a novel periplasmic [Fe] hydrogenase, which are integral members of the electron transport system. This genome sequence represents a critical step in the elucidation of the pathways for reduction (and bioremediation) of pollutants such as uranium (U) and chromium (Cr), and offers a starting point for defining this organism's complex electron transport systems and metal ion-reducing capabilities.
ESTHER : Heidelberg_2002_Nat.Biotechnol_20_1118
PubMedSearch : Heidelberg_2002_Nat.Biotechnol_20_1118
PubMedID: 12368813
Gene_locus related to this paper: sheon-BIOH , sheon-LYPA , sheon-PIP , sheon-PTRB , sheon-q8ej95 , sheon-SO0071 , sheon-SO0614 , sheon-SO0616 , sheon-SO0801 , sheon-SO0880 , sheoe-SO0967 , sheon-SO1006 , sheon-SO1224 , sheon-SO1310 , sheon-SO1534 , sheon-SO1539 , sheon-SO1686 , sheon-SO1743 , sheon-SO1976 , sheon-SO1999 , sheon-SO2024 , sheon-SO2047 , sheon-SO2055 , sheon-SO2223 , sheon-SO2333 , sheon-SO2473 , sheon-SO2582 , sheon-SO2753 , sheon-SO2934 , sheon-SO3025 , sheon-SO3900 , sheon-SO3990 , sheon-SO4252 , sheon-SO4400 , sheon-SO4537 , sheon-SO4543 , sheon-SO4574 , sheon-SO4618 , sheon-SO4650 , sheon-SOA0048 , shefn-SfSFGH , sheon-ym51

Title : Noncholine esterases and cholinesterases [letter\; comment] -
Author(s) : Lee C
Ref : Journal of Clinical Anesthesia , 6 :166 , 1994
PubMedID: 7911307

Title : PD 142676 (CI 1002), a novel anticholinesterase and muscarinic antagonist - Emmerling_1994_Mol.Neurobiol_9_93
Author(s) : Emmerling MR , Gregor VE , Schwarz RD , Scholten JD , Callahan MJ , Lee C , Moore CJ , Raby C , Lipinski WJ , Davis RE
Ref : Molecular Neurobiology , 9 :93 , 1994
Abstract : Inhibition of brain acetylcholinesterase (AChE) can provide relief from the cognitive loss associated with Alzheimer's disease (AD). However, unwanted peripheral side effects often limit the usefulness of the available anticholinesterases. Recently, we identified a dihydroquinazoline compound, PD 142676 (CI 1002) that is a potent anticholinesterase and a functional muscarinic antagonist at higher concentrations. Peripherally, PD 142676, unlike other anticholinesterases, inhibits gastrointestinal motility in rats, an effect consistent with its muscarinic antagonist properties. Centrally, the compound acts as a cholinomimetic. In rats, PD 142676 decreases core body temperature. It also increases neocortical arousal, as measured by quantitative electroencephalography, and cortical acetylcholine levels, measured by in vivo microdialysis. The compound improves the performance of C57/B10j mice in a water maze task and of aged rhesus monkeys in a delayed match-to-sample task involving short-term memory. The combined effect of AChE inhibition and muscarinic antagonism distinguishes PD 142676 from other anticholinesterases, and may be useful in treating the cognitive dysfunction of AD and produce fewer peripheral side effects.
ESTHER : Emmerling_1994_Mol.Neurobiol_9_93
PubMedSearch : Emmerling_1994_Mol.Neurobiol_9_93
PubMedID: 7888109

Title : Essential fatty acid deficiency in cultured SK-N-SH human neuroblastoma cells - Stubbs_1992_Adv.Exp.Med.Biol_318_171
Author(s) : Stubbs EB, Jr. , Carlson RO , Lee C , Fisher SK , Hajra AK , Agranoff BW
Ref : Advances in Experimental Medicine & Biology , 318 :171 , 1992
Abstract : SK-N-SH neuroblastoma cells grown under standard culture conditions contain significant amounts of Mead acid (20:3 omega 9) in phospholipids, indicating essential fatty acid (EFA) deficiency. The amount of esterified 20:3 omega 9 was augmented by growth in a chemically defined EFA-free medium, whereas its presence could be virtually eliminated by supplementation of the culture medium with either arachidonic (20:4 omega 6; AA), eicosapentaenoic (20:5 omega 3; EPA), or linolenic (18:3 omega 3) acids. Substitution of Mead acid for omega 6 fatty acids, particularly evident in phosphatidylinositol (PI), indicates a compensatory replacement of omega 9 for omega 6 fatty acids during EFA deficiency. Studies evaluating [3H]scopolamine binding to the M3 muscarinic acetylcholine receptors (mAChRs) present in these neurotumor cells as well as effects of carbachol on phosphoinositide turnover and intracellular Ca2+ mobilization, indicate that the biosubstitution of 20:4 omega 6 with 20:3 omega 9 does not detectably impair these measures of signal transduction. Stimulation of mAChRs with carbachol increased the cellular mass of diacylglycerol (DAG) approximately 60%. On the basis of distinctive fatty acid "signatures" of each of the phospholipid classes, it is concluded that the DAG initially released following muscarinic stimulation is derived from phosphoinositide breakdown. After several minutes, however, a significant amount of DAG comes from phosphatidylcholine (PC) as well. In contrast to DAG, the composition of phosphatidate (PA) following receptor stimulation closely resembles that of the phosphoinositides, even at the later time points examined. These results support a selective phosphorylation of DAG arising from the stimulated breakdown of phosphoinositides, favoring the conservation of the 1-stearoyl, 2-arachidonoyl (or 20:3 omega 9) moiety.
ESTHER : Stubbs_1992_Adv.Exp.Med.Biol_318_171
PubMedSearch : Stubbs_1992_Adv.Exp.Med.Biol_318_171
PubMedID: 1636488

Title : Quantitative analysis of molecular species of diacylglycerol and phosphatidate formed upon muscarinic receptor activation of human SK-N-SH neuroblastoma cells - Lee_1991_J.Biol.Chem_266_22837
Author(s) : Lee C , Fisher SK , Agranoff BW , Hajra AK
Ref : Journal of Biological Chemistry , 266 :22837 , 1991
Abstract : Quantitative changes in the total mass and the molecular species of 1,2-diacyl-sn-glycerol (DAG) and phosphatidic acid (PA) formed upon muscarinic receptor activation were studied in cultured human SK-N-SH neuroblastoma cells. DAG was isolated from the total lipid extracts of carbachol (CCh)-stimulated and unstimulated cells and after benzoylation, was subjected to reverse phase high performance liquid chromatography to separate the component species. The molecular species of DAG were identified by analyzing the fatty acid composition of each separated fraction by gas chromatography, and their total and individual masses were quantified from the known amount of an internal standard, 1,2-distearoyl-sn-glycerol, added during the extraction of the lipid. Relatively high basal levels of DAG (1.5 nmol/mg protein) are present in these cells, and addition of CCh elicited a 50-60% increase in the total amounts of DAG within 5 min. The increase was biphasic: an initial major peak at 5 min was followed by a sustained increase that persisted for at least 30 min. An increase in DAG was elicited by both full and partial muscarinic agonists and was blocked by atropine. The presence of extracellular Ca2+ was necessary for muscarinic receptor-activated formation of DAG. To determine the source of the DAG, the molecular species of the major phospholipids present in SK-N-SH cells were also analyzed. The phospholipids were first enzymatically hydrolyzed to DAGs which were then analyzed as described above. A number of unusual fatty acids, the major one being 20:3 (n-9), were present in these lipids especially in the phosphoinositides and also in the DAG formed after CCh stimulation. Within 5 s of CCh stimulation there were transient increases in the DAG species representative of phosphoinositides. By 5 min the newly formed molecular species of DAG resembled a mixture of phosphoinositides and phosphatidylcholine (PC). Quantitative comparison of the molecular species compositions of phosphoinositides, PC, and newly formed DAGs indicated that at time periods up to 10 min, approximately 30% of the DAG originated from the phosphoinositides and the rest from PC. At longer intervals (greater than 20 min), most (85%) of DAGs originated from PC. Activation of muscarinic receptors in SK-N-SH cells also elicited an increase in PA (200% in 5 min). A quantitative molecular species analysis, using 1,2-distearoyl-sn-glycerol-3-P as internal standard, was performed by enzymatic (alkaline phosphatase) hydrolysis of PA to DAG and subsequent analysis.(ABSTRACT TRUNCATED AT 400 WORDS)
ESTHER : Lee_1991_J.Biol.Chem_266_22837
PubMedSearch : Lee_1991_J.Biol.Chem_266_22837
PubMedID: 1744076