Author Report for: Hou SNo contact information in database for Hou S
Chen Z, Yu X, Chen L, Xu L, Cai Y, Hou S, Zheng M, Liu F Ref: Ann Transl Med, 10:303, 2022 : PubMed ESTHER: Chen_2022_Ann.Transl.Med_10_303 PubMedSearch: Chen 2022 Ann.Transl.Med 10 303 PubMedID: 35433950 Abstract BACKGROUND: Alzheimer's disease (AD) is thought to be a complex, multifactorial syndrome with many related molecular lesions contributing to its pathogenesis. Thus, multi-target-directed ligands are considered an effective way of treating AD. This study sought to evaluate 8-aminoquinoline-melatonin derivatives as effective multifunctional agents for AD. METHODS: Thioflavin-T fluorescence assays were used to detect the inhibitory potency of 8-aminoquinoline-melatonin hybrids (a1-a5, b1-b5, and c1-c5) on self- and acetylcholinesterase (AChE)-induced amyloid-beta (Abeta) aggregation. The AChE and butyrylcholinesterase (BuChE) inhibitory potency within the compounds was evaluated by Ellman's assays. Methyl thiazolyl tetrazolium (MTT) assays were performed to evaluate the cytotoxicity of the compounds to C17.2 cells. MTT assay was used to detect the cell viability of HT22 cells to evaluate the antioxidant effect of the compounds. Metal chelation property was measured by ultraviolet-visible spectrophotometry. RESULTS: Compounds c3 and c5 had superior inhibitory activity against self-induced Abeta aggregation (with inhibitory rates of 41.4+/-2.1 and 25.5+/-3.2 at 10 microM, respectively) compared to the other compounds. Compounds in the carbamate group (i.e., a4, a5, b4, b5, c4, and c5) showed significant BuChE inhibitory activity and excellent selectivity over AChE. Most of the compounds exhibited low cytotoxicity in the C17.2 cells. Notably, a2, a3, b2, and b3 and series c (c1-c5) exhibited strong protective effects. Additionally, a3 and c1 specifically chelated with copper ions. CONCLUSIONS: Taking all of the promising results together, 8-aminoquinoline-melatonin hybrids can serve as lead molecules in the further development of new multi-functional anti-AD agents. Title: Long non-coding RNA ABHD11-AS1 facilitates the progression of cervical cancer by competitively binding to miR-330-5p and upregulating MARK2 Hou S, Zhang X, Yang J Ref: Experimental Cell Research, 410:112929, 2022 : PubMed ESTHER: Hou_2022_Exp.Cell.Res_410_112929 PubMedSearch: Hou 2022 Exp.Cell.Res 410 112929 PubMedID: 34793775 Abstract Cervical cancer (CC) is among the most prevalent gynecological malignancies. Participation of long non-coding RNA (lncRNA) in modulating biological behaviors of CC cells has been confirmed. However, the function of lncRNA ABHD11 antisense RNA 1 (ABHD11-AS1) in CC is still unclear. RT-qPCR and Western blot were performed for measuring RNA and protein levels. Functional assays were done to evaluate ABHD11-AS1 influences on cell proliferation, apoptosis, invasion and migration. After the verification of ABHD11-AS1 distribution in CC cells, mechanism assays were conducted to study the interaction of relative RNAs. ABHD11-AS1 expression was abnormally high in CC cells. In vitro experiments showed ABHD11-AS1 downregulation restrained CC cell malignant phenotypes. In vivo experiments proved ABHD11-AS1 knockdown impeded tumor growth. Moreover, miR-330-5p was corroborated to bind with ABHD11-AS1 in CC cells and microtubule affinity regulating kinase 2 (MARK2) was confirmed to be targeted by miR-330-5p. MiR-330-5p inhibition or MARK2 overexpression could countervail the suppressive effect of ABHD11-AS1 knockdown on CC cell malignant behaviors. We found that ABHD11-AS1 facilitated CC tumorigenesis through competitively sequestering miR-330-5p to upregulate MARK2, indicating ABHD11-AS1 as a potential biomarker in CC. Title: Huperzine-A Improved Animal Behavior in Cuprizone-Induced Mouse Model by Alleviating Demyelination and Neuroinflammation Zhang T, Kim MJ, Wu X, Yang HJ, Yuan H, Huang S, Yoon SM, Kim KN, Park S and Wang J <46 more author(s)> Zhang T, Kim MJ, Wu X, Yang HJ, Yuan H, Huang S, Yoon SM, Kim KN, Park S, Zhang Y, Yao J, Yin K, Liu Z, Deng C, Liu J, Hou S, Zhang H, Yu D, Zhao N, Zhao R, Chen S, Zhang ZP, Bai X, Cui WB, Chen XH, Liu X, Zhi DJ, Zhang ZX, Fei DQ, Wang DS, Zhang X, Wang Y, Zhu H, Zhong Z, Zhang CY, Tan XH, Yang HH, Jin L, Hong JR, Zhou Y, Huang XT, Zhang M, Xiang R, Glorieux C, Huang P, Young C, Morishita Y, Kim K, Kabil OO, Clarke OB, Di Jeso B, Arvan P, Wang D, Sun J, Wu S, Wang J (- 46) Ref: Int J Mol Sci, 23:, 2022 : PubMed ESTHER: Zhang_2022_Int.J.Mol.Sci_23_ PubMedSearch: Zhang 2022 Int.J.Mol.Sci 23 PubMedID: 35328781 35563299 35743309 35887300 35897843 36233022 36362390 36555825 Abstract Huperzine A (HupA) is a natural acetylcholinesterase inhibitor (AChEI) with the advantages of high efficiency, selectivity as well as reversibility and can exhibit significant therapeutic effects against certain neurodegenerative diseases. It is also beneficial in reducing the neurological impairment and neuroinflammation of experimental autoimmune encephalomyelitis (EAE), a classic model for multiple sclerosis (MS). However, whether HupA can directly regulate oligodendrocyte differentiation and maturation and promote remyelination has not been investigated previously. In this study, we have analyzed the potential protective effects of HupA on the demylination model of MS induced by cuprizone (CPZ). It was found that HupA significantly attenuated anxiety-like behavior, as well as augmented motor and cognitive functions in CPZ mice. It also decreased demyelination and axonal injury in CPZ mice. Moreover, in CPZ mice, HupA increased mRNA levels of the various anti-inflammatory cytokines (Arg1, CD206) while reducing the levels of different pro-inflammatory cytokines (iNOS, IL-1beta, IL-18, CD16, and TNF-alpha). Mecamylamine, a nicotinic acetylcholinergic receptor antagonist, could effectively reverse the effects of HupA. Therefore, we concluded that HupA primarily exerts its therapeutic effects on multiple sclerosis through alleviating demyelination and neuroinflammation. Title: Computational Design and Crystal Structure of a Highly Efficient Benzoylecgonine Hydrolase Chen X, Deng X, Zhang Y, Wu Y, Yang K, Li Q, Wang J, Yao W, Tong J and Yao J <2 more author(s)> Chen X, Deng X, Zhang Y, Wu Y, Yang K, Li Q, Wang J, Yao W, Tong J, Xie T, Hou S, Yao J (- 2) Ref: Angew Chem Int Ed Engl, :, 2021 : PubMed ESTHER: Chen_2021_Angew.Chem.Int.Ed.Engl__ PubMedSearch: Chen 2021 Angew.Chem.Int.Ed.Engl PubMedID: 34351032 Inhibitor(s) related to this paper: Benzoic-acid Abstract Benzoylecgonine (BZE) is the major toxic metabolite of cocaine, and is responsible for the long-term cocaine-induced toxicity due to its long residence time in humans. BZE is also the main contaminant following cocaine consumption, representing a risk to our environment and non-target organisms. Here, we identified the bacterial cocaine esterase (CocE) as a BZE-metabolizing enzyme (BZEase), which can degrade BZE into biological inactive metabolites (ecgonine and benzoic acid). CocE was redesigned by a reactant-state-based enzyme design theory. An encouraging mutant denoted as BZEase2, presented a >400-fold improved catalytic efficiency against BZE compared with wild-type (WT) CocE. In vivo , a single dose of BZEase2 (1 mg/kg, IV) could eliminate nearly all BZE within only two minutes, suggesting the enzyme have the potential for cocaine overdose treatment and BZE elimination in the environment by accelerating BZE clearance. The crystal structure of a designed BZEase was determined, providing additional insights in support of our simulation results. Title: Overexpression of serum lncRNA-ABHD11-AS1 as poor prognosis of patients with papillary thyroid carcinoma Hou S, Zhuang YY, Lin QY, Chen Z, Zhao HG, Zhang L, Lin CH Ref: Exp Mol Pathol, 121:104658, 2021 : PubMed ESTHER: Hou_2021_Exp.Mol.Pathol_121_104658 PubMedSearch: Hou 2021 Exp.Mol.Pathol 121 104658 PubMedID: 34102210 Abstract This paper was aimed at exploring the correlation of long non-coding RNA (lncRNA)-ABHD11 Antisense RNA1 (ABHD11-AS1) with the poor prognosis of patients with papillary thyroid carcinoma (PTC) and at investigating its effects on the survival of PTC cells. Serum was respectively collected from 64 PTC patients who were admitted to our hospital (PTC group) and from 50 healthy controls who underwent physical examinations (HC group) both from April 2011 to April 2015. The expression levels of ABHD11-AS1 in the serum were detected, and the values of it for diagnosis and prognosis (5-year follow-ups) were analyzed. The knockdown and overexpression models of ABHD11-AS1 in were constructed to explore the effects of the models on their proliferation, cycles and apoptosis. According to the data, the expression levels of serum ABHD11-AS1 in the PTC patients were remarkably higher than those in the healthy controls, and the area under the curve (AUC) for distinguishing the patients from the controls was 0.920. In the analysis of prognosis, the levels in patients with a poor prognosis were remarkably higher than those in patients with a good prognosis. According to the curves of overall survival rates (OSRs), the high levels of ABHD11-AS1 were remarkably correlated with the poor prognosis (a lower 5-year OSR). COX analysis showed that TNM staging, lymph node metastasis and ABHD11-AS1 were the independent prognostic factors of PTC patients. In the cell experiments, knocking down ABHD11-AS1 remarkably inhibited PTC cells from proliferation, arrested them in G0/G1 phase, and induced their apoptosis, negatively affecting their survival indices. Overexpressing this RNA had positive effects on the survival indices. Taken together, high levels of serum ABHD11-AS1 are related to the poor prognosis of PTC patients, and knocking down its expression can inhibit the survival of PTC cells. Title: Evaluation of the cholinesterase activity of a potential therapeutic cocaine esterase for cocaine overdose Hou S, Zhang Y, Zhu Y, Zhang C, Kong Y, Chen X, Chen R, Yin X, Xie T Ref: Drug Alcohol Depend, 202:168, 2019 : PubMed ESTHER: Hou_2019_Drug.Alcohol.Depend_202_168 PubMedSearch: Hou 2019 Drug.Alcohol.Depend 202 168 PubMedID: 31352306 Abstract BACKGROUND: Cocaine is a commonly abused drug and there is no approved medication specifically to treat its addiction or overdose. Bacterial cocaine esterase (CocE)-derived RBP-8000 is currently under clinical development for cocaine overdose treatment. It is proven to be effective for human use to accelerate cocaine metabolism into physiologically inactive products. Besides cocaine, RBP-8000 may hydrolyze the neurotransmitter acetylcholine (ACh), however, no study has reported its cholinesterase activity. The present study aims to examine RBP-8000's cholinesterase activity and substrate selectivity to address the potential concern that this enzyme therapy might produce cholinergic side-effects. METHODS: Both computational modeling and experimental kinetic analysis were carried out to characterize the potential cholinesterase activity of RBP-8000. Substrates interacting with RBP-8000 were modeled for their enzyme-substrate binding complexes. In vitro enzymatic kinetic parameters were measured using Ellman's colorimetric assay and analyzed by Michaelis-Menten kinetics. RESULTS: It is the first demonstration that RBP-8000 catalyzes the hydrolysis of acetylthiocholine (ATC). However, its catalytic efficiency (kcat/KM) against ATC is 1000-fold and 5000-fold lower than it against cocaine at 25 degrees C and 37 degrees C, respectively, suggesting RBP-8000 has the desired substrate selectivity for cocaine over ACh. CONCLUSION: Given the fact that clinically relevant dose of RBP-8000 displays insignificant cholinesterase activity relative to endogenous cholinesterases in human, administration of RBP-8000 is unlikely to produce any significant cholinergic side-effects. This study provides supplemental evidences in support of further development of RBP-8000 towards a clinically used pharmacotherapy for cocaine overdose. Title: Fluorescence sensor for facile and visual detection of organophosphorus pesticides using AIE fluorogens-SiO2-MnO2 sandwich nanocomposites Wu X, Wang P, Hou S, Wu P, Xue J Ref: Talanta, 198:8, 2019 : PubMed ESTHER: Wu_2019_Talanta_198_8 PubMedSearch: Wu 2019 Talanta 198 8 PubMedID: 30876606 Abstract Organophosphorus pesticides (OPs) are frequently for pest control in the agriculture industry. Accumulation of OPs is harmful to the environment and human health. Thus, facile and portable detection of organophosphorus pesticides is of great importance. Among these methods, the fluorescence assay holds the advantages of high sensitivity, simplicity, nondestructive properties. Conventional fluorophores have the drawbacks of poor photostability and low signal-to-noise ratio due to their aggregation-caused quenching drawbacks at high concentration or in the aggregate state. Aggregation-induced emission fluorogens (AIEgens) are one key to develop next-generation fluorescence sensor due to their high emission efficiency in the aggregated state. 1,2-bis[4-(3-sulfonatopropoxyl) phenyl]-1,2-diphenylethene (BSPOTPE) is a typical AIE molecule containing two hydroxyl group. In this study, a fluorescence sensor based on BSPOTPE-SiO2-MnO2 sandwich nanocomposites was fabricated. Thiocholine (TCh), which produced from acetylthiocholine(ATCh) by the hydrolysis of acetylcholinesterase (AChE), can "turn on" the fluorescence sensor. Based on the inhibition effect of OPs on AChE activity and the corresponding "turn off" effect on the fluorescence sensor, an AIE-based assay for OPs determination was developed. The fabricated sensor for paraoxon determination has a good linear relationship in the range of 1-100mug/L and the LOD of 1mug/L. Moreover, a simple, convenient fluorescence strip for visual semi-quantitative of OPs was fabricated, indicating this "on-off" fluorescent sensor is promising for on-site and infield detection. Title: Genome-wide association studies reveal genetic loci associated with plasma cholinesterase activity in ducks Xu Y, Liu H, Jiang Y, Fan W, Hu J, Zhang Y, Guo Z, Xie M, Huang W and Hou S <2 more author(s)> Xu Y, Liu H, Jiang Y, Fan W, Hu J, Zhang Y, Guo Z, Xie M, Huang W, Liu X, Zhou Z, Hou S (- 2) Ref: Anim Genet, 50:287, 2019 : PubMed ESTHER: Xu_2019_Anim.Genet_50_287 PubMedSearch: Xu 2019 Anim.Genet 50 287 PubMedID: 30994195 Gene_locus related to this paper: anapl-BCHE Abstract Plasma cholinesterase (PCHE) activity is an important auxiliary test in human clinical medicine. It can distinguish liver diseases from non-liver diseases and help detect organophosphorus poisoning. Animal experiments have confirmed that PCHE activity is associated with obesity and hypertension and changes with physiological changes in an animal's body. The objective of this study was to locate the genetic loci responsible for PCHE activity variation in ducks. PCHE activity of Pekin duck x mallard F2 ducks at 3 and 8 weeks of age were analyzed, and genome-wide association studies were conducted. A region of about 1.5 Mb (21.8-23.3 Mb) on duck chromosome 9 was found to be associated with PCHE activity at both 3 and 8 weeks of age. The top SNP, g.22643979C>T in the butyrylcholinesterase (BCHE) gene, was most highly associated with PCHE activity at 3 weeks (-logP = 21.45) and 8 weeks (-logP = 27.60) of age. For the top SNP, the strong associations of CC and CT genotypes with low PCHE activity and the TT genotype with high PCHE activity indicates the dominant inheritance of low PCHE activity. Problems with block inheritance or linkage exist in this region. This study supports that BCHE is a functional gene for determining PCHE levels in ducks and that the genetic variations around this gene can cause phenotypic variations of PCHE activity. Title: Crystal structure of a lipase from Streptomyces sp. strain W007 - implications for thermostability and regiospecificity Zhao Z, Hou S, Lan D, Wang X, Liu J, Khan FI, Wang Y Ref: Febs J, 284:3506, 2017 : PubMed ESTHER: Zhao_2017_FEBS.J_284_3506 PubMedSearch: Zhao 2017 FEBS.J 284 3506 PubMedID: 28857479 Gene_locus related to this paper: 9actn-h0b8d4 Abstract MAS1 from marine Streptomyces sp. strain W007 belongs to the bacterial lipase I.7 subfamily and is characterized as a thermostable and nonregiospecific lipase. To shed light on the catalytic mechanism of MAS1, we determined its crystal structure with closed conformation in two crystal forms at 2.3 A resolution. MAS1 adopts the canonical alpha/beta hydrolase core fold with its catalytic triad being formed by S109, D200 and H232. Structural analysis and biochemical assays revealed that disulfide bonds and salt bridges play a vital role in the thermostability of MAS1. In addition, we discovered that the replacement of H108 with a tryptophan converts MAS1 from a nonregiospecific to an sn-1,3-specific lipase, suggesting the functional importance of the second position from the conserved pentapeptide motif in defining the regiospecificity of MAS1. Our present study provides insights into the molecular basis for the thermostability and regiospecificity of MAS1, and it may aid in the rational design of thermostable or regiospecific lipases for potential industrial applications. DATABASE: Structural data are available in the Protein Data Bank database under the accession numbers 5H6B and 5H6G. Title: Kinetic characterization of a cocaine hydrolase engineered from mouse butyrylcholinesterase Chen X, Huang X, Geng L, Xue L, Hou S, Zheng X, Brimijoin S, Zheng F, Zhan CG Ref: Biochemical Journal, 466:243, 2015 : PubMed ESTHER: Chen_2015_Biochem.J_466_243 PubMedSearch: Chen 2015 Biochem.J 466 243 PubMedID: 25486543 Gene_locus related to this paper: human-BCHE Inhibitor(s) related to this paper: Cocaine Abstract Mouse butyrylcholinesterase (mBChE) and an mBChE-based cocaine hydrolase (mCocH, i.e. the A199S/S227A/S287G/A328W/Y332G mutant) have been characterized for their catalytic activities against cocaine, i.e. naturally occurring (-)-cocaine, in comparison with the corresponding human BChE (hBChE) and an hBChE-based cocaine hydrolase (hCocH, i.e. the A199S/F227A/S287G/A328W/Y332G mutant). It has been demonstrated that mCocH and hCocH have improved the catalytic efficiency of mBChE and hBChE against (-)-cocaine by ~8- and ~2000-fold respectively, although the catalytic efficiencies of mCocH and hCocH against other substrates, including acetylcholine (ACh) and butyrylthiocholine (BTC), are close to those of the corresponding wild-type enzymes mBChE and hBChE. According to the kinetic data, the catalytic efficiency (kcat/KM) of mBChE against (-)-cocaine is comparable with that of hBChE, but the catalytic efficiency of mCocH against (-)-cocaine is remarkably lower than that of hCocH by ~250-fold. The remarkable difference in the catalytic activity between mCocH and hCocH is consistent with the difference between the enzyme-(-)-cocaine binding modes obtained from molecular modelling. Further, both mBChE and hBChE demonstrated substrate activation for all of the examined substrates [(-)-cocaine, ACh and BTC] at high concentrations, whereas both mCocH and hCocH showed substrate inhibition for all three substrates at high concentrations. The amino-acid mutations have remarkably converted substrate activation of the enzymes into substrate inhibition, implying that the rate-determining step of the reaction in mCocH and hCocH might be different from that in mBChE and hBChE. Title: A genomic perspective to assessing quality of mass-reared SIT flies used in Mediterranean fruit fly (Ceratitis capitata) eradication in California Calla B, Hall B, Hou S, Geib SM Ref: BMC Genomics, 15:98, 2014 : PubMed ESTHER: Calla_2014_BMC.Genomics_15_98 PubMedSearch: Calla 2014 BMC.Genomics 15 98 PubMedID: 24495485 Gene_locus related to this paper: cerca-w8bwm7, cerca-w8c4w6, cerca-w8buv2, cerca-w8brr0 Abstract BACKGROUND: Temperature sensitive lethal (tsl) mutants of the tephritid C. capitata are used extensively in control programs involving sterile insect technique in California. These flies are artificially reared and treated with ionizing radiation to render males sterile for further release en masse into the field to compete with wild males and disrupt establishment of invasive populations. Recent research suggests establishment of C. capitata in California, despite the fact that over 250 million sterile flies are released weekly as part of the state's preventative program. In this project, genome-level quality assessment was performed, measured as expression differences between the Vienna-7 tsl mutants used in SIT programs and wild flies. RNA-seq was performed to provide a genome-wide map of the messenger RNA populations in C. capitata, and to investigate significant expression changes in Vienna-7 mass reared flies. Title: Amino-acid mutations to extend the biological half-life of a therapeutically valuable mutant of human butyrylcholinesterase Fang L, Hou S, Xue L, Zheng F, Zhan CG Ref: Chemico-Biological Interactions, 214C:18, 2014 : PubMed ESTHER: Fang_2014_Chem.Biol.Interact_214C_18 PubMedSearch: Fang 2014 Chem.Biol.Interact 214C 18 PubMedID: 24582612 Gene_locus related to this paper: human-BCHE Inhibitor(s) related to this paper: Cocaine Abstract Cocaine is a widely abused and addictive drug without an FDA-approved medication. Our recently designed and discovered cocaine hydrolase, particularly E12-7 engineered from human butyrylcholinesterase (BChE), has the promise of becoming a valuable cocaine abuse treatment. An ideal anti-cocaine therapeutic enzyme should have not only a high catalytic efficiency against cocaine, but also a sufficiently long biological half-life. However, recombinant human BChE and the known BChE mutants have a much shorter biological half-life compared to the native human BChE. The present study aimed to extend the biological half-life of the cocaine hydrolase without changing its high catalytic activity against cocaine. Our strategy was to design possible amino-acid mutations that can introduce cross-subunit disulfide bond(s) and, thus, change the distribution of the oligomeric forms and extend the biological half-life. Three new BChE mutants (E364-532, E377-516, and E535) were predicted to have a more stable dimer structure with the desirable cross-subunit disulfide bond(s) and, therefore, a different distribution of the oligomeric forms and a prolonged biological half-life. The rational design was followed by experimental tests in vitro and in vivo, confirming that the rationally designed new BChE mutants, i.e. E364-532, E377-516, and E535, indeed had a remarkably different distribution of the oligomeric forms and prolonged biological half-life in rats from approximately 7 to approximately 13h without significantly changing the catalytic activity against (-)-cocaine. This is the first demonstration that rationally designed amino-acid mutations can significantly prolong the biological half-life of a high-activity enzyme without significantly changing the catalytic activity. Title: Rational design, preparation, and characterization of a therapeutic enzyme mutant with improved stability and function for cocaine detoxification Fang L, Chow KM, Hou S, Xue L, Chen X, Rodgers DW, Zheng F, Zhan CG Ref: ACS Chemical Biology, 9:1764, 2014 : PubMed ESTHER: Fang_2014_ACS.Chem.Biol_9_1764 PubMedSearch: Fang 2014 ACS.Chem.Biol 9 1764 PubMedID: 24919140 Gene_locus related to this paper: rhosm-cocE Inhibitor(s) related to this paper: Cocaine Abstract Cocaine esterase (CocE) is known as the most efficient natural enzyme for cocaine hydrolysis. The major obstacle to the clinical application of wild-type CocE is the thermoinstability with a half-life of only approximately 12 min at 37 degrees C. The previously designed T172R/G173Q mutant (denoted as enzyme E172-173) with an improved in vitro half-life of approximately 6 h at 37 degrees C is currently in clinical trial Phase II for cocaine overdose treatment. Through molecular modeling and dynamics simulation, we designed and characterized a promising new mutant of E172-173 with extra L196C/I301C mutations (denoted as enzyme E196-301) to produce cross-subunit disulfide bonds that stabilize the dimer structure. The cross-subunit disulfide bonds were confirmed by X-ray diffraction. The designed L196C/I301C mutations have not only considerably extended the in vitro half-life at 37 degrees C to >100 days, but also significantly improved the catalytic efficiency against cocaine by approximately 150%. In addition, the thermostable E196-301 can be PEGylated to significantly prolong the residence time in mice. The PEGylated E196-301 can fully protect mice from a lethal dose of cocaine (180 mg/kg, LD100) for at least 3 days, with an average protection time of approximately 94h. This is the longest in vivo protection of mice from the lethal dose of cocaine demonstrated within all studies using an exogenous enzyme reported so far. Hence, E196-301 may be developed to become a more valuable therapeutic enzyme for cocaine abuse treatment, and it demonstrates that a general design strategy and protocol to simultaneously improve both the stability and function are feasible for rational protein drug design. Title: Kinetic characterization of human butyrylcholinesterase mutants for the hydrolysis of cocaethylene Hou S, Zhan M, Zheng X, Zhan CG, Zheng F Ref: Biochemical Journal, 460:447, 2014 : PubMed ESTHER: Hou_2014_Biochem.J_460_447 PubMedSearch: Hou 2014 Biochem.J 460 447 PubMedID: 24870023 Abstract It is known that the majority of cocaine users also consume alcohol. Alcohol can react with cocaine to produce a significantly more cytotoxic compound, cocaethylene. Hence a truly valuable cocaine-metabolizing enzyme as treatment for cocaine abuse/overdose should be efficient for not only cocaine itself, but also cocaethylene. The catalytic parameters (kcat and KM) of human BChE (butyrylcholinesterase) and two mutants (known as cocaine hydrolases E14-3 and E12-7) for cocaethylene are characterized in the present study, for the first time, in comparison with those for cocaine. On the basis of the obtained kinetic data, wild-type human BChE has a lower catalytic activity for cocaethylene (kcat=3.3 min-1, KM=7.5 muM and kcat/KM=4.40x105 M-1.min-1) compared with its catalytic activity for (-)-cocaine. E14-3 and E12-7 have a considerably improved catalytic activity against cocaethylene compared with the wild-type BChE. E12-7 is identified as the most efficient enzyme for hydrolysing cocaethylene in addition to its high activity for (-)-cocaine. E12-7 has an 861-fold improved catalytic efficiency for cocaethylene (kcat=3600 min-1, KM=9.5 muM and kcat/KM=3.79x108 M-1.min-1). It has been demonstrated that E12-7 as an exogenous enzyme can indeed rapidly metabolize cocaethylene in rats. Further kinetic modelling has suggested that E12-7 with an identical concentration as that of the endogenous BChE in human plasma can effectively eliminate (-)-cocaine, cocaethylene and norcocaine in simplified kinetic models of cocaine abuse and overdose associated with the concurrent use of cocaine and alcohol. Title: Synthesis and pharmacological characterization of new neuronal nicotinic acetylcholine receptor ligands derived from Sazetidine-A Liu Y, Paige M, Olson TT, Al-Muhtasib N, Xie T, Hou S, White MP, Cordova A, Guo JL and Brown ML <2 more author(s)> Liu Y, Paige M, Olson TT, Al-Muhtasib N, Xie T, Hou S, White MP, Cordova A, Guo JL, Kellar KJ, Xiao Y, Brown ML (- 2) Ref: Bioorganic & Medicinal Chemistry Lett, 24:2954, 2014 : PubMed ESTHER: Liu_2014_Bioorg.Med.Chem.Lett_24_2954 PubMedSearch: Liu 2014 Bioorg.Med.Chem.Lett 24 2954 PubMedID: 24844195 Abstract The enantiomers of two analogs of Sazetidine-A as well as several other novel biosteric analogues were synthesized. Their binding affinities at three major nAChRs subtypes and selectivity profiles were determined. Though many (S)-enantiomers of Sazetidine-A analogs have high binding affinities and good subtype selectivities, it is not a general rule that (S)-enantiomers are better than their (R) counterparts. Compound 11, of which the ethynyl group was replaced by its' bioisostere-the triazole via click chemistry, showed a high binding affinity to alpha4beta2 subtype (Ki=1.3 nM) and better selectivity to the alpha4beta2 subtype over alpha3beta4 subtype with that of Sazetidine-A. The azide compound 15, a potential photoaffinity label, showed improved high selectivity and similar binding property profile with that of Sazetidine-A. The biaryl analog 17 exhibited a much lower affinity as compared to Sazetidine-A indicating the importance of a 'long tail' side chain for alpha4beta2 nAChR binding. Title: Kinetic characterization of high-activity mutants of human butyrylcholinesterase for the cocaine metabolite norcocaine Zhan M, Hou S, Zhan CG, Zheng F Ref: Biochemical Journal, 457:197, 2014 : PubMed ESTHER: Zhan_2014_Biochem.J_457_197 PubMedSearch: Zhan 2014 Biochem.J 457 197 PubMedID: 24125115 Abstract It has been known that cocaine produces its toxic and physiological effects through not only cocaine itself, but also norcocaine formed from cocaine oxidation catalysed by microsomal CYP (cytochrome P450) 3A4 in the human liver. The catalytic parameters (kcat and Km) of human BChE (butyrylcholinesterase) and its three mutants (i.e. A199S/S287G/A328W/Y332G, A199S/F227A/S287G/A328W/E441D and A199S/F227A/S287G/A328W/Y332G) for norcocaine have been characterized in the present study for the first time and compared with those for cocaine. On the basis of the obtained kinetic data, wild-type human BChE has a significantly lower catalytic activity for norcocaine (kcat=2.8 min-1, Km=15 muM and kcat/Km=1.87x105 M-1.min-1) compared with its catalytic activity for (-)-cocaine. The BChE mutants examined in the present study have considerably improved catalytic activities against both cocaine and norcocaine compared with the wild-type enzyme. Within the enzymes examined in the present study, the A199S/F227A/S287G/A328W/Y332G mutant (CocH3) is identified as the most efficient enzyme for hydrolysing both cocaine and norcocaine. CocH3 has a 1080-fold improved catalytic efficiency for norcocaine (kcat=2610 min-1, Km=13 muM and kcat/Km=2.01x108 M-1.min-1) and a 2020-fold improved catalytic efficiency for cocaine. It has been demonstrated that CocH3 as an exogenous enzyme can rapidly metabolize norcocaine, in addition to cocaine, in rats. Further kinetic modelling has suggested that CocH3 with an identical concentration with that of the endogenous BChE in human plasma can effectively eliminate both cocaine and norcocaine in a simplified kinetic model of cocaine abuse. Title: A highly efficient cocaine-detoxifying enzyme obtained by computational design Zheng F, Xue L, Hou S, Liu J, Zhan M, Yang W, Zhan CG Ref: Nat Commun, 5:3457, 2014 : PubMed ESTHER: Zheng_2014_Nat.Commun_5_3457 PubMedSearch: Zheng 2014 Nat.Commun 5 3457 PubMedID: 24643289 Gene_locus related to this paper: human-BCHE Inhibitor(s) related to this paper: Cocaine Abstract Compared with naturally occurring enzymes, computationally designed enzymes are usually much less efficient, with their catalytic activities being more than six orders of magnitude below the diffusion limit. Here we use a two-step computational design approach, combined with experimental work, to design a highly efficient cocaine hydrolysing enzyme. We engineer E30-6 from human butyrylcholinesterase (BChE), which is specific for cocaine hydrolysis, and obtain a much higher catalytic efficiency for cocaine conversion than for conversion of the natural BChE substrate, acetylcholine (ACh). The catalytic efficiency of E30-6 for cocaine hydrolysis is comparable to that of the most efficient known naturally occurring hydrolytic enzyme, acetylcholinesterase, the catalytic activity of which approaches the diffusion limit. We further show that E30-6 can protect mice from a subsequently administered lethal dose of cocaine, suggesting the enzyme may have therapeutic potential in the setting of cocaine detoxification or cocaine abuse. Title: Substrate selectivity of high-activity mutants of human butyrylcholinesterase Hou S, Xue L, Yang W, Fang L, Zheng F, Zhan CG Ref: Org Biomol Chem, 11:7477, 2013 : PubMed ESTHER: Hou_2013_Org.Biomol.Chem_11_7477 PubMedSearch: Hou 2013 Org.Biomol.Chem 11 7477 PubMedID: 24077614 Abstract Cocaine is one of the most addictive drugs, and there is still no FDA (Food and Drug Administration)-approved medication specific for cocaine abuse. A promising therapeutic strategy is to accelerate cocaine metabolism, producing biologically inactive metabolites via a route similar to the primary cocaine-metabolizing pathway, i.e. cocaine hydrolysis catalyzed by butyrylcholinesterase (BChE) in plasma. However, the native BChE has a low catalytic efficiency against the abused cocaine, i.e. (-)-cocaine. Our recently designed and discovered A199S/F227A/S287G/A328W/Y332G mutant and other mutants of human BChE have a considerably improved catalytic efficiency against (-)-cocaine. In the present study, we carried out both computational modeling and experimental kinetic analysis on the catalytic activities of these promising new BChE mutants against other known substrates, including neurotransmitter acetylcholine (ACh), acetylthiocholine (ATC), butyrylthiocholine (BTC), and (+)-cocaine, in comparison with the corresponding catalytic activity against (-)-cocaine. Both the computational modeling and kinetic analysis have consistently revealed that all the examined amino acid mutations only considerably improve the catalytic efficiency of human BChE against (-)-cocaine, without significantly improving the catalytic efficiency of the enzyme against any of the other substrates examined. In particular, all the examined BChE mutants have a slightly lower catalytic efficiency against neurotransmitter ACh compared to the wild-type BChE. This observation gives us confidence in developing an anti-cocaine enzyme therapy by using one of these BChE mutants, particularly the A199S/F227A/S287G/A328W/Y332G mutant. Title: Cultivation and complete genome sequencing of Gloeobacter kilaueensis sp. nov., from a lava cave in Kilauea Caldera, Hawai'i Saw JH, Schatz M, Brown MV, Kunkel DD, Foster JS, Shick H, Christensen S, Hou S, Wan X, Donachie SP Ref: PLoS ONE, 8:e76376, 2013 : PubMed ESTHER: Saw_2013_PLoS.ONE_8_E76376 PubMedSearch: Saw 2013 PLoS.ONE 8 E76376 PubMedID: 24194836 Gene_locus related to this paper: 9cyan-u5qk25, 9cyan-u5qet4, 9cyan-u5qd16, 9cyan-u5qqd5 Abstract The ancestor of Gloeobacter violaceus PCC 7421(T) is believed to have diverged from that of all known cyanobacteria before the evolution of thylakoid membranes and plant plastids. The long and largely independent evolutionary history of G. violaceus presents an organism retaining ancestral features of early oxygenic photoautotrophs, and in whom cyanobacteria evolution can be investigated. No other Gloeobacter species has been described since the genus was established in 1974 (Rippka et al., Arch Microbiol 100:435). Gloeobacter affiliated ribosomal gene sequences have been reported in environmental DNA libraries, but only the type strain's genome has been sequenced. However, we report here the cultivation of a new Gloeobacter species, G. kilaueensis JS1(T), from an epilithic biofilm in a lava cave in Kilauea Caldera, Hawai'i. The strain's genome was sequenced from an enriched culture resembling a low-complexity metagenomic sample, using 9 kb paired-end 454 pyrosequences and 400 bp paired-end Illumina reads. The JS1(T) and G. violaceus PCC 7421(T) genomes have little gene synteny despite sharing 2842 orthologous genes; comparing the genomes shows they do not belong to the same species. Our results support establishing a new species to accommodate JS1(T), for which we propose the name Gloeobacter kilaueensis sp. nov. Strain JS1(T) has been deposited in the American Type Culture Collection (BAA-2537), the Scottish Marine Institute's Culture Collection of Algae and Protozoa (CCAP 1431/1), and the Belgian Coordinated Collections of Microorganisms (ULC0316). The G. kilaueensis holotype has been deposited in the Algal Collection of the US National Herbarium (US 217948). The JS1(T) genome sequence has been deposited in GenBank under accession number CP003587. The G+C content of the genome is 60.54 mol%. The complete genome sequence of G. kilaueensis JS1(T) may further understanding of cyanobacteria evolution, and the shift from anoxygenic to oxygenic photosynthesis. Title: Catalytic activities of a cocaine hydrolase engineered from human butyrylcholinesterase against (+)- and (-)-cocaine Xue L, Hou S, Yang W, Fang L, Zheng F, Zhan CG Ref: Chemico-Biological Interactions, 203:57, 2013 : PubMed ESTHER: Xue_2013_Chem.Biol.Interact_203_57 PubMedSearch: Xue 2013 Chem.Biol.Interact 203 57 PubMedID: 22917637 Inhibitor(s) related to this paper: Cocaine Abstract It can be argued that an ideal anti-cocaine medication would be one that accelerates cocaine metabolism producing biologically inactive metabolites via a route similar to the primary cocaine-metabolizing pathway, i.e., hydrolysis catalyzed by butyrylcholinesterase (BChE) in plasma. However, wild-type BChE has a low catalytic efficiency against naturally occurring (-)-cocaine. Interestingly, wild-type BChE has a much higher catalytic activity against unnatural (+)-cocaine. According to available positron emission tomography (PET) imaging analysis using [(11)C](-)-cocaine and [(11)C](+)-cocaine tracers in human subjects, only [(11)C](-)-cocaine was observed in the brain, whereas no significant [(11)C](+)-cocaine signal was observed in the brain. The available PET data imply that an effective therapeutic enzyme for treatment of cocaine abuse could be an exogenous cocaine-metabolizing enzyme with a catalytic activity against (-)-cocaine comparable to that of wild-type BChE against (+)-cocaine. Our recently designed A199S/F227A/S287G/A328 W/Y332G mutant of human BChE has a considerably improved catalytic efficiency against (-)-cocaine and has been proven active in vivo. In the present study, we have characterized the catalytic activities of wild-type BChE and the A199S/F227A/S287G/A328 W/Y332G mutant against both (+)- and (-)-cocaine at the same time under the same experimental conditions. Based on the obtained kinetic data, the A199S/F227A/S287G/A328 W/Y332G mutant has a similarly high catalytic efficiency (kcat/KM) against (+)- and (-)-cocaine, and indeed has a catalytic efficiency (kcat/KM=1.84x10(9)M(-1)min(-1)) against (-)-cocaine comparable to that (kcat/KM=1.37x10(9)M(-1)min(-1)) of wild-type BChE against (+)-cocaine. Thus, the mutant may be used to effectively prevent (-)-cocaine from entering brain and producing physiological effects in the enzyme-based treatment of cocaine abuse. Title: Preparation and in vivo characterization of a cocaine hydrolase engineered from human butyrylcholinesterase for metabolizing cocaine Xue L, Hou S, Tong M, Fang L, Chen X, Jin Z, Tai HH, Zheng F, Zhan CG Ref: Biochemical Journal, 453:447, 2013 : PubMed ESTHER: Xue_2013_Biochem.J_453_447 PubMedSearch: Xue 2013 Biochem.J 453 447 PubMedID: 23849058 Abstract Cocaine is a widely abused drug without an FDA (Food and Drug Administration)-approved medication. It has been recognized that an ideal anti-cocaine medication would accelerate cocaine metabolism producing biologically inactive metabolites via a route similar to the primary cocaine-metabolizing pathway, i.e. human BChE (butyrylcholinesterase)-catalysed hydrolysis. However, the native human BChE has a low catalytic activity against cocaine. We recently designed and discovered a BChE mutant (A199S/F227A/S287G/A328W/Y332G) with a high catalytic activity (kcat=5700 min-1, Km=3.1 muM) specifically for cocaine, and the mutant was proven effective in protecting mice from acute cocaine toxicity of a lethal dose of cocaine (180 mg/kg of body weight, LD100). Further characterization in animal models requires establishment of a high-efficiency stable cell line for the BChE mutant production at a relatively larger scale. It has been extremely challenging to develop a high-efficiency stable cell line expressing BChE or its mutant. In the present study, we successfully developed a stable cell line efficiently expressing the BChE mutant by using a lentivirus-based repeated-transduction method. The scaled-up protein production enabled us to determine for the first time the in vivo catalytic activity and the biological half-life of this high-activity mutant of human BChE in accelerating cocaine clearance. In particular, it has been demonstrated that the BChE mutant (administered to mice 1 min prior to cocaine) can quickly metabolize cocaine and completely eliminate cocaine-induced hyperactivity in rodents, implying that the BChE mutant may be developed as a promising therapeutic agent for cocaine abuse treatment. Title: Amperometric acetylcholine biosensor based on self-assembly of gold nanoparticles and acetylcholinesterase on the sol-gel/multi-walled carbon nanotubes/choline oxidase composite-modified platinum electrode Hou S, Ou Z, Chen Q, Wu B Ref: Biosensors & Bioelectronics, 33:44, 2012 : PubMed ESTHER: Hou_2012_Biosens.Bioelectron_33_44 PubMedSearch: Hou 2012 Biosens.Bioelectron 33 44 PubMedID: 22230694 Abstract A novel acetylcholinesterase (AChE)/choline oxidase (ChOx) bienzyme amperometric acetylcholine biosensor based on gold nanoparticles (AuNPs) and multi-walled carbon nanotubes (MWCNTs) has been successfully developed by self-assembly process in combination of sol-gel technique. A thiolated aqueous silica sol containing MWCNTs and ChOx was first dropped on the surface of a cleaned Pt electrode, and then AuNPs were assembled with the thiolated sol-gel network. Finally, the alternate deposition of poly (diallyldimethylammonium chloride) (PDDA) and AChE was repeated to assemble different layers of PDDA-AChE on the electrode for optimizing AChE loading. Among the resulting biosensors, the biosensor based on two layers of PDDA-AChE multilayer films showed the best performance. It exhibited a wide linear range, high sensitivity and fast amperometric response, which were 0.005-0.4mM, 3.395 muA/mM, and within 15s, respectively. The biosensor showed long-term stability and acceptable reproducibility. More importantly, this study could provide a simple and effective multienzyme immobilization platform for meeting the demand of the effective immobilization enzyme on the electrode surface. Title: Tools to kill: genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolina Islam MS, Haque MS, Islam MM, Emdad EM, Halim A, Hossen QM, Hossain MZ, Ahmed B, Rahim S and Alam M <5 more author(s)> Islam MS, Haque MS, Islam MM, Emdad EM, Halim A, Hossen QM, Hossain MZ, Ahmed B, Rahim S, Rahman MS, Alam MM, Hou S, Wan X, Saito JA, Alam M (- 5) Ref: BMC Genomics, 13:493, 2012 : PubMed ESTHER: Islam_2012_BMC.Genomics_13_493 PubMedSearch: Islam 2012 BMC.Genomics 13 493 PubMedID: 22992219 Gene_locus related to this paper: macph-k2rpg5, macph-k2rib9, macph-k2rk99, macph-k2rr60, macph-k2qwn3, macph-k2rda2, macph-k2rh46, macph-k2rhf0, macph-k2rls3, macph-k2rps6, macph-k2rpy1, macph-k2rtn6, macph-k2rty0, macph-k2rub9, macph-k2rvj5, macph-k2ryd3, macph-k2s0u2, macph-k2s1j3, macph-k2s4t0, macph-k2s6a5, macph-k2s713, macph-k2s7d0, macph-k2s7l1, macph-k2s9s2, macph-k2sg04, macph-k2si26, macph-k2r678, macph-k2sls1, macph-k2rt33, macph-k2rb00, macph-k2scp3, macph-k2r291, macph-k2r695, macph-k2r9q4, macph-k2res7, macph-k2s7y7, macph-k2rnn6 Abstract BACKGROUND: Macrophomina phaseolina is one of the most destructive necrotrophic fungal pathogens that infect more than 500 plant species throughout the world. It can grow rapidly in infected plants and subsequently produces a large amount of sclerotia that plugs the vessels, resulting in wilting of the plant. Title: Complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12 Ong SY, Pratap CB, Wan X, Hou S, Abdul Rahman AY, Saito JA, Nath G, Alam M Ref: Journal of Bacteriology, 194:2115, 2012 : PubMed ESTHER: Ong_2012_J.Bacteriol_194_2115 PubMedSearch: Ong 2012 J.Bacteriol 194 2115 PubMedID: 22461552 Gene_locus related to this paper: salty-STY1441, salty-YFBB Abstract We report here the complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12, a clinical isolate obtained from a typhoid carrier in India. Title: Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium Saw JH, Yuryev A, Kanbe M, Hou S, Young AG, Aizawa S, Alam M Ref: Stand Genomic Sci, 6:84, 2012 : PubMed ESTHER: Saw_2012_Stand.Genomic.Sci_6_84 PubMedSearch: Saw 2012 Stand.Genomic.Sci 6 84 PubMedID: 22675601 Gene_locus related to this paper: sapgl-h6kz52, sapgl-h6l1q6 Abstract Saprospira grandis is a coastal marine bacterium that can capture and prey upon other marine bacteria using a mechanism known as 'ixotrophy'. Here, we present the complete genome sequence of Saprospira grandis str. Lewin isolated from La Jolla beach in San Diego, California. The complete genome sequence comprises a chromosome of 4.35 Mbp and a plasmid of 54.9 Kbp. Genome analysis revealed incomplete pathways for the biosynthesis of nine essential amino acids but presence of a large number of peptidases. The genome encodes multiple copies of sensor globin-coupled rsbR genes thought to be essential for stress response and the presence of such sensor globins in Bacteroidetes is unprecedented. A total of 429 spacer sequences within the three CRISPR repeat regions were identified in the genome and this number is the largest among all the Bacteroidetes sequenced to date. Title: Crystal structure of a mono- and diacylglycerol lipase from Malassezia globosa reveals a novel lid conformation and insights into the substrate specificity Xu T, Liu L, Hou S, Xu J, Yang B, Wang Y, Liu J Ref: J Struct Biol, 178:363, 2012 : PubMed ESTHER: Xu_2012_J.Struct.Biol_178_363 PubMedSearch: Xu 2012 J.Struct.Biol 178 363 PubMedID: 22484238 Gene_locus related to this paper: malgo-a8puy1 Abstract Most lipases contain a lid domain to shield the hydrophobic binding site from the water environment. The lid, mostly in helical form, can undergo a conformational change to expose the active cleft during the interfacial activation. Here we report the crystal structures of Malassezia globosa LIP1 (SMG1) at 1.45 and 2.60 resolution in two crystal forms. The structures present SMG1 in its closed form, with a novel lid in loop conformation. SMG1 is one of the few members in the fungal lipase family that has been found to be strictly specific for mono- and diacylglycerol. To date, the mechanism for this substrate specificity remains largely unknown. To investigate the substrate binding properties, we built a model of SMG1 in open conformation. Based on this model, we found that the two bulky hydrophobic residues adjacent to the catalytic site and the N-terminal hinge region of the lid both may act as steric hindrances for triacylglycerols binding. These unique structural features of SMG1 will provide a better understanding on the substrate specificity of mono- and diacylglycerol lipases and a platform for further functional study of this enzyme. Title: Optimal production and biochemical properties of a lipase from Candida albicans Lan D, Hou S, Yang N, Whiteley C, Yang B, Wang Y Ref: Int J Mol Sci, 12:7216, 2011 : PubMed ESTHER: Lan_2011_Int.J.Mol.Sci_12_7216 PubMedSearch: Lan 2011 Int.J.Mol.Sci 12 7216 PubMedID: 22072943 Abstract Lipases from microorganisms have multi-faceted properties and play an important role in ever-growing modern biotechnology and, consequently, it is of great significance to develop new ones. In the present work, a lipase gene from Candida albicans (CaLIP10) was cloned and two non-unusual CUG serine codons were mutated into universal codons, and its expression in Pichia pastoris performed optimally, as shown by response surface methodology. Optimal conditions were: initial pH of culture 6.86, temperature 25.53 degrees C, 3.48% of glucose and 1.32% of yeast extract. The corresponding maximal lipolytic activity of CaLIP10 was 8.06 U/mL. The purified CaLIP10 showed maximal activity at pH 8.0 and 25 degrees C, and a good resistance to non-ionic surfactants and polar organic solvent was noticed. CaLIP10 could effectively hydrolyze coconut oil, but exhibited no obvious preference to the fatty acids with different carbon length, and diacylglycerol was accumulated in the reaction products, suggesting that CaLIP10 is a potential lipase for the oil industry. Title: Design, preparation, and characterization of high-activity mutants of human butyrylcholinesterase specific for detoxification of cocaine Xue L, Ko MC, Tong M, Yang W, Hou S, Fang L, Liu J, Zheng F, Woods JH and Zhan CG <1 more author(s)> Xue L, Ko MC, Tong M, Yang W, Hou S, Fang L, Liu J, Zheng F, Woods JH, Tai HH, Zhan CG (- 1) Ref: Molecular Pharmacology, 79:290, 2011 : PubMed ESTHER: Xue_2011_Mol.Pharmacol_79_290 PubMedSearch: Xue 2011 Mol.Pharmacol 79 290 PubMedID: 20971807 Abstract Cocaine is a widely abused drug without a U.S. Food and Drug Administration-approved medication. There is a recognized, promising anticocaine medication to accelerate cocaine metabolism, producing biologically inactive metabolites via a route similar to the primary cocaine-metabolizing pathway [i.e., cocaine hydrolysis catalyzed by butyrylcholinesterase (BChE) in plasma]. An ideal, therapeutically valuable mutant of human BChE should have not only a significantly improved catalytic activity against (-)-cocaine but also certain selectivity for (-)-cocaine over neurotransmitter acetylcholine (ACh), such that one would not expect systemic administration of the BChE mutant to interrupt cholinergic transmission. The present study accounting for the mutation-caused changes of the catalytic activities of BChE against both (-)-cocaine and ACh by means of molecular modeling and site-directed mutagenesis has led to identification of three BChE mutants that have not only a considerably improved catalytic efficiency against (-)-cocaine but also the desirable selectivity for (-)-cocaine over ACh. Two representative BChE mutants have been confirmed to be potent in actual protection of mice from acute toxicity (convulsion and lethality) of a lethal dose of cocaine (180 mg/kg). Pretreatment with the BChE mutant (i.e., 1 min before cocaine administration) dose-dependently protected mice against cocaine-induced convulsions and lethality. In particular, all mice pretreated with the mutant (e.g., 0.02 mg or more of A199S/F227A/S287G/A328W/E441D BChE) survived. The in vivo data reveal the primary factor (i.e., the relative catalytic efficiency), determining the efficacy in practical protection of mice from the acute cocaine toxicity and future direction for further improving the efficacy of the enzyme in the cocaine overdose treatment. Title: The genome of a songbird Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A, Searle S, White S, Vilella AJ and Wilson RK <72 more author(s)> Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK (- 72) Ref: Nature, 464:757, 2010 : PubMed ESTHER: Warren_2010_Nature_464_757 PubMedSearch: Warren 2010 Nature 464 757 PubMedID: 20360741 Gene_locus related to this paper: taegu-b5fyu7, taegu-BCHE, taegu-h0z4h9, taegu-h0z9w8, taegu-h0zat6, taegu-h0ze48, taegu-h0zha8, taegu-h0zkr8, taegu-h0zqp3, taegu-h0zz82, taegu-h0zqs1, taegu-h0yy64, taegu-h0yv40, taegu-h0yyt1, taegu-h0zcc8, taegu-h0z3k5, taegu-h0yw95, taegu-h0zkm7, taegu-h1a198, taegu-h0z6w2, taegu-h0zl93, taegu-h0zt33, taegu-h0yp71, taegu-h0ypu5, taegu-h1a048, taegu-h0ztq1, fical-u3kau2, 9pass-a0a093qu66, taegu-h0z7g0, fical-u3jnn0, taegu-h0zb80, taegu-h0zb89, taegu-h0z994, taegu-h0ztj6 Abstract The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour. Title: Design of high-activity mutants of human butyrylcholinesterase against (-)-cocaine: structural and energetic factors affecting the catalytic efficiency Zheng F, Yang W, Xue L, Hou S, Liu J, Zhan CG Ref: Biochemistry, 49:9113, 2010 : PubMed ESTHER: Zheng_2010_Biochemistry_49_9113 PubMedSearch: Zheng 2010 Biochemistry 49 9113 PubMedID: 20886866 Abstract The present study was aimed to explore the correlation between the protein structure and catalytic efficiency of butyrylcholinesterase (BChE) mutants against (-)-cocaine by modeling the rate-determining transition state (TS1), i.e., the transition state for the first step of chemical reaction process, of (-)-cocaine hydrolysis catalyzed by various mutants of human BChE in comparison with the wild type. Molecular modeling of the TS1 structures revealed that mutations on certain nonactive site residues can indirectly affect the catalytic efficiency of the enzyme against (-)-cocaine through enhancing or weakening the overall hydrogen bonding between the carbonyl oxygen of (-)-cocaine benzoyl ester and the oxyanion hole of the enzyme. Computational insights and predictions were supported by the catalytic activity data obtained from wet experimental tests on the mutants of human BChE, including five new mutants reported for the first time. The BChE mutants with at least approximately 1000-fold improved catalytic efficiency against (-)-cocaine compared to the wild-type BChE are all associated with the TS1 structures having stronger overall hydrogen bonding between the carbonyl oxygen of (-)-cocaine benzoyl ester and the oxyanion hole of the enzyme. The combined computational and experimental data demonstrate a reasonable correlation relationship between the hydrogen-bonding distances in the TS1 structure and the catalytic efficiency of the enzyme against (-)-cocaine. Title: Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia Hou S, Makarova KS, Saw JH, Senin P, Ly BV, Zhou Z, Ren Y, Wang J, Galperin MY and Alam M <11 more author(s)> Hou S, Makarova KS, Saw JH, Senin P, Ly BV, Zhou Z, Ren Y, Wang J, Galperin MY, Omelchenko MV, Wolf YI, Yutin N, Koonin EV, Stott MB, Mountain BW, Crowe MA, Smirnova AV, Dunfield PF, Feng L, Wang L, Alam M (- 11) Ref: Biol Direct, 3:26, 2008 : PubMed ESTHER: Hou_2008_Biol.Direct_3_26 PubMedSearch: Hou 2008 Biol.Direct 3 26 PubMedID: 18593465 Gene_locus related to this paper: meti4-b3dw86, meti4-b3dx04 Abstract BACKGROUND: The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. We have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the Verrucomicrobia, strain V4, isolated from the Hell's Gate geothermal area in New Zealand. Similar organisms were independently isolated from geothermal systems in Italy and Russia. RESULTS: We report the complete genome sequence of strain V4, the first one from a representative of the Verrucomicrobia. Isolate V4, initially named "Methylokorus infernorum" (and recently renamed Methylacidiphilum infernorum) is an autotrophic bacterium with a streamlined genome of ~2.3 Mbp that encodes simple signal transduction pathways and has a limited potential for regulation of gene expression. Central metabolism of M. infernorum was reconstructed almost completely and revealed highly interconnected pathways of autotrophic central metabolism and modifications of C1-utilization pathways compared to other known methylotrophs. The M. infernorum genome does not encode tubulin, which was previously discovered in bacteria of the genus Prosthecobacter, or close homologs of any other signature eukaryotic proteins. Phylogenetic analysis of ribosomal proteins and RNA polymerase subunits unequivocally supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a single clade, the PVC superphylum, despite dramatically different gene content in members of these three groups. Comparative-genomic analysis suggests that evolution of the M. infernorum lineage involved extensive horizontal gene exchange with a variety of bacteria. The genome of M. infernorum shows apparent adaptations for existence under extremely acidic conditions including a major upward shift in the isoelectric points of proteins. CONCLUSION: The results of genome analysis of M. infernorum support the monophyly of the PVC superphylum. M. infernorum possesses a streamlined genome but seems to have acquired numerous genes including those for enzymes of methylotrophic pathways via horizontal gene transfer, in particular, from Proteobacteria. REVIEWERS: This article was reviewed by John A. Fuerst, Ludmila Chistoserdova, and Radhey S. Gupta. Title: Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1 Saw JH, Mountain BW, Feng L, Omelchenko MV, Hou S, Saito JA, Stott MB, Li D, Zhao G and Alam M <8 more author(s)> Saw JH, Mountain BW, Feng L, Omelchenko MV, Hou S, Saito JA, Stott MB, Li D, Zhao G, Wu J, Galperin MY, Koonin EV, Makarova KS, Wolf YI, Rigden DJ, Dunfield PF, Wang L, Alam M (- 8) Ref: Genome Biol, 9:R161, 2008 : PubMed ESTHER: Saw_2008_Genome.Biol_9_R161 PubMedSearch: Saw 2008 Genome.Biol 9 R161 PubMedID: 19014707 Gene_locus related to this paper: anofw-b7ghw8, anofw-b7gk10, anofw-b7gk45, anofw-b7gln5, anofw-b7glx5, anofw-b7gm70 Abstract BACKGROUND: Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life. RESULTS: We report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres. CONCLUSIONS: Microbial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli. Title: Genome analysis of the platypus reveals unique signatures of evolution Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grutzner F, Belov K, Miller W, Clarke L and Wilson RK <94 more author(s)> Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grutzner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, Lopez-Otin C, Ordonez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefevre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK (- 94) Ref: Nature, 453:175, 2008 : PubMed ESTHER: Warren_2008_Nature_453_175 PubMedSearch: Warren 2008 Nature 453 175 PubMedID: 18464734 Gene_locus related to this paper: ornan-f6s0q0, ornan-f6ty74, ornan-f6u2k2, ornan-f6uve1, ornan-f6vpb6, ornan-f6ybp3, ornan-f7bgu8, ornan-f7ct41, ornan-f7cza1, ornan-f7ejp8, ornan-f7exu1, ornan-f7f392, ornan-f7f9y6, ornan-f6ve87, ornan-f7f1d9, ornan-f6z3l1, ornan-f6r3f9, ornan-f6r3g8, ornan-f6vs71, ornan-f7g4v8 Abstract We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation. Title: Generation and annotation of the DNA sequences of human chromosomes 2 and 4 Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K and Wilson RK <111 more author(s)> Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Kremitzki C, Oddy L, Du H, Sun H, Bradshaw-Cordum H, Ali J, Carter J, Cordes M, Harris A, Isak A, Van Brunt A, Nguyen C, Du F, Courtney L, Kalicki J, Ozersky P, Abbott S, Armstrong J, Belter EA, Caruso L, Cedroni M, Cotton M, Davidson T, Desai A, Elliott G, Erb T, Fronick C, Gaige T, Haakenson W, Haglund K, Holmes A, Harkins R, Kim K, Kruchowski SS, Strong CM, Grewal N, Goyea E, Hou S, Levy A, Martinka S, Mead K, McLellan MD, Meyer R, Randall-Maher J, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Shah N, Swearengen-Shahid S, Snider J, Strong JT, Thompson J, Yoakum M, Leonard S, Pearman C, Trani L, Radionenko M, Waligorski JE, Wang C, Rock SM, Tin-Wollam AM, Maupin R, Latreille P, Wendl MC, Yang SP, Pohl C, Wallis JW, Spieth J, Bieri TA, Berkowicz N, Nelson JO, Osborne J, Ding L, Sabo A, Shotland Y, Sinha P, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Jones TA, She X, Ciccarelli FD, Izaurralde E, Taylor J, Schmutz J, Myers RM, Cox DR, Huang X, McPherson JD, Mardis ER, Clifton SW, Warren WC, Chinwalla AT, Eddy SR, Marra MA, Ovcharenko I, Furey TS, Miller W, Eichler EE, Bork P, Suyama M, Torrents D, Waterston RH, Wilson RK (- 111) Ref: Nature, 434:724, 2005 : PubMed ESTHER: Hillier_2005_Nature_434_724 PubMedSearch: Hillier 2005 Nature 434 724 PubMedID: 15815621 Gene_locus related to this paper: human-ABHD1, human-LDAH, human-ABHD18, human-KANSL3, human-PGAP1, human-PREPL Abstract Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions. Title: Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy Hou S, Saw JH, Lee KS, Freitas TA, Belisle C, Kawarabayasi Y, Donachie SP, Pikina A, Galperin MY and Alam M <12 more author(s)> Hou S, Saw JH, Lee KS, Freitas TA, Belisle C, Kawarabayasi Y, Donachie SP, Pikina A, Galperin MY, Koonin EV, Makarova KS, Omelchenko MV, Sorokin A, Wolf YI, Li QX, Keum YS, Campbell S, Denery J, Aizawa S, Shibata S, Malahoff A, Alam M (- 12) Ref: Proc Natl Acad Sci U S A, 101:18036, 2004 : PubMed ESTHER: Hou_2004_Proc.Natl.Acad.Sci.U.S.A_101_18036 PubMedSearch: Hou 2004 Proc.Natl.Acad.Sci.U.S.A 101 18036 PubMedID: 15596722 Gene_locus related to this paper: idilo-q5qtt2, idilo-q5qun1, idilo-q5qv96, idilo-q5qvg7, idilo-q5qvi6, idilo-q5qvn0, idilo-q5qvy7, idilo-q5qw13, idilo-q5qwm4, idilo-q5qwp3, idilo-q5qwr5, idilo-q5qx36, idilo-q5qx78, idilo-q5qx89, idilo-q5qxa5, idilo-q5qxf1, idilo-q5qxp3, idilo-q5qy75, idilo-q5qy90, idilo-q5qyl8, idilo-q5qym1, idilo-q5qzc0, idilo-q5qzv2, idilo-q5qzv4, idilo-q5qzz6, idilo-q5r0d5, idilo-q5r0h2, idilo-q5r0u5, idilo-q5r036, idilo-q5r068, idilo-q5r196 Abstract We report the complete genome sequence of the deep-sea gamma-proteobacterium, Idiomarina loihiensis, isolated recently from a hydrothermal vent at 1,300-m depth on the Loihi submarine volcano, Hawaii. The I. loihiensis genome comprises a single chromosome of 2,839,318 base pairs, encoding 2,640 proteins, four rRNA operons, and 56 tRNA genes. A comparison of I. loihiensis to the genomes of other gamma-proteobacteria reveals abundance of amino acid transport and degradation enzymes, but a loss of sugar transport systems and certain enzymes of sugar metabolism. This finding suggests that I. loihiensis relies primarily on amino acid catabolism, rather than on sugar fermentation, for carbon and energy. Enzymes for biosynthesis of purines, pyrimidines, the majority of amino acids, and coenzymes are encoded in the genome, but biosynthetic pathways for Leu, Ile, Val, Thr, and Met are incomplete. Auxotrophy for Val and Thr was confirmed by in vivo experiments. The I. loihiensis genome contains a cluster of 32 genes encoding enzymes for exopolysaccharide and capsular polysaccharide synthesis. It also encodes diverse peptidases, a variety of peptide and amino acid uptake systems, and versatile signal transduction machinery. We propose that the source of amino acids for I. loihiensis growth are the proteinaceous particles present in the deep sea hydrothermal vent waters. I. loihiensis would colonize these particles by using the secreted exopolysaccharide, digest these proteins, and metabolize the resulting peptides and amino acids. In summary, the I. loihiensis genome reveals an integrated mechanism of metabolic adaptation to the constantly changing deep-sea hydrothermal ecosystem. Title: The DNA sequence of human chromosome 7 Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S and Wilson RK <97 more author(s)> Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK (- 97) Ref: Nature, 424:157, 2003 : PubMed ESTHER: Hillier_2003_Nature_424_157 PubMedSearch: Hillier 2003 Nature 424 157 PubMedID: 12853948 Gene_locus related to this paper: human-ABHD11, human-ACHE, human-CPVL, human-DPP6, human-MEST Abstract Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated with various forms of cancer. Here we present more than 153 million base pairs representing 99.4% of the euchromatic sequence of chromosome 7, the first metacentric chromosome completed so far. The sequence has excellent concordance with previously established physical and genetic maps, and it exhibits an unusual amount of segmentally duplicated sequence (8.2%), with marked differences between the two arms. Our initial analyses have identified 1,150 protein-coding genes, 605 of which have been confirmed by complementary DNA sequences, and an additional 941 pseudogenes. Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame. Title: Complete genome sequence of Salmonella enterica serovar Typhimurium LT2 McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M and Wilson RK <16 more author(s)> McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M, Du F, Hou S, Layman D, Leonard S, Nguyen C, Scott K, Holmes A, Grewal N, Mulvaney E, Ryan E, Sun H, Florea L, Miller W, Stoneking T, Nhan M, Waterston R, Wilson RK (- 16) Ref: Nature, 413:852, 2001 : PubMed ESTHER: McClelland_2001_Nature_413_852 PubMedSearch: McClelland 2001 Nature 413 852 PubMedID: 11677609 Gene_locus related to this paper: salen-OPDB, salti-q8z717, salty-AES, salty-BIOH, salty-ENTF, salty-FES, salty-IROD, salty-IROE, salty-P74847, salty-PLDB, salty-STM0332, salty-STM2547, salty-STM3079, salty-STM4506, salty-STY1441, salty-STY2428, salty-STY3846, salty-yafa, salty-YBFF, salty-ycfp, salty-YFBB, salty-YHET, salty-YJFP, salty-YQIA Abstract Salmonella enterica subspecies I, serovar Typhimurium (S. typhimurium), is a leading cause of human gastroenteritis, and is used as a mouse model of human typhoid fever. The incidence of non-typhoid salmonellosis is increasing worldwide, causing millions of infections and many deaths in the human population each year. Here we sequenced the 4,857-kilobase (kb) chromosome and 94-kb virulence plasmid of S. typhimurium strain LT2. The distribution of close homologues of S. typhimurium LT2 genes in eight related enterobacteria was determined using previously completed genomes of three related bacteria, sample sequencing of both S. enterica serovar Paratyphi A (S. paratyphi A) and Klebsiella pneumoniae, and hybridization of three unsequenced genomes to a microarray of S. typhimurium LT2 genes. Lateral transfer of genes is frequent, with 11% of the S. typhimurium LT2 genes missing from S. enterica serovar Typhi (S. typhi), and 29% missing from Escherichia coli K12. The 352 gene homologues of S. typhimurium LT2 confined to subspecies I of S. enterica-containing most mammalian and bird pathogens-are useful for studies of epidemiology, host specificity and pathogenesis. Most of these homologues were previously unknown, and 50 may be exported to the periplasm or outer membrane, rendering them accessible as therapeutic or vaccine targets. Title: Genome sequence of Halobacterium species NRC-1 Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V and DasSarma S <33 more author(s)> Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J, Swartzell S, Weir D, Hall J, Dahl TA, Welti R, Goo YA, Leithauser B, Keller K, Cruz R, Danson MJ, Hough DW, Maddocks DG, Jablonski PE, Krebs MP, Angevine CM, Dale H, Isenbarger TA, Peck RF, Pohlschroder M, Spudich JL, Jung KW, Alam M, Freitas T, Hou S, Daniels CJ, Dennis PP, Omer AD, Ebhardt H, Lowe TM, Liang P, Riley M, Hood L, DasSarma S (- 33) Ref: Proc Natl Acad Sci U S A, 97:12176, 2000 : PubMed ESTHER: Ng_2000_Proc.Natl.Acad.Sci.U.S.A_97_12176 PubMedSearch: Ng 2000 Proc.Natl.Acad.Sci.U.S.A 97 12176 PubMedID: 11016950 Gene_locus related to this paper: halsp-est, halsp-metx, halsp-VNG0492H, halsp-VNG0675C, halsp-VNG1418C, halsp-VNG1833C, halsp-Vng6296c, halsp-YUXL Abstract We report the complete sequence of an extreme halophile, Halobacterium sp. NRC-1, harboring a dynamic 2,571,010-bp genome containing 91 insertion sequences representing 12 families and organized into a large chromosome and 2 related minichromosomes. The Halobacterium NRC-1 genome codes for 2,630 predicted proteins, 36% of which are unrelated to any previously reported. Analysis of the genome sequence shows the presence of pathways for uptake and utilization of amino acids, active sodium-proton antiporter and potassium uptake systems, sophisticated photosensory and signal transduction pathways, and DNA replication, transcription, and translation systems resembling more complex eukaryotic organisms. Whole proteome comparisons show the definite archaeal nature of this halophile with additional similarities to the Gram-positive Bacillus subtilis and other bacteria. The ease of culturing Halobacterium and the availability of methods for its genetic manipulation in the laboratory, including construction of gene knockouts and replacements, indicate this halophile can serve as an excellent model system among the archaea. | |||||||
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