DOCSLIB.ORG

Using MALDI-TOF MS Analysis for Rapid Discrimination of MRSA MLST

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Using MALDI-TOF MS analysis for rapid discrimination of MRSA MLST types Jang-Jih Lu1,2,Tsui-Ping Liu1, Shih-Cheng Chang1,2 1Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan 2Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan Email: [email protected] 73 0:F8 MS Ra w 71 0:F9 MS Ra w 5000 6422.794 6000 Intens.[a.u.] Intens.[a.u.] Introduction 4000 Results ST5 ST5 4000 3000 2978.985 2000 6551.531 Staphylococcus aureus is one of the common causes of 3027.802 3054.785 2964.900 3175.943 2000 Table 1: MRSA and MSSA associated peaks by MALDI TOF 1000 community-associated infections and health care related 234 0:F1 MS Ra w 234 0:F1 MS Ra w 3005.919 MRSA(129 isolates) MSSA(77 isolates) 5000 6000 Intens.[a.u.] Intens.[a.u.] pathogen. It can usually cause wound infection, ST45 4000 ST45 6549.206 4000 3000 MS peaks (m/z) no. of isolate % of isolate no. of isolate % of isolate 6420.525 osteomyelitis, and even serious invasive infections, such as 2000 6610.628 2000 2978.373 3053.663 3174.805 2415 67 51.9 2 2.6 1000 sepsis and pneumonia. Epidemiology studies have shown 86 0:E4 MS Ra w 70 0:E5 MS Ra w 3058.565 5000 2431 65 50.4 0 0 3074.390 6000 Intens.[a.u.] Intens.[a.u.] that there are close relationship between the results of ST59 4000 6550.723 ST59 4000 3000 2879 51 39.5 2 2.6 6422.151 genotyping from multilocus sequence typing (MLST) and 2000 2000 characteristics of MRSA strains, including hospital- 6593 77 59.7 7 9.1 1000 200 0:E8 MS Ra w 38 0:E11 MS Ra w Appear of any above 103 79.8 11 14.3 2978.890 5000 6000 Intens.[a.u.] Intens.[a.u.] 6421.658 acquired, community-associated strain and even the 2965.568 ST239 4000 ST239 peaks 4000 3000 none of above peaks 6590.270 26 20.1 66 85.7 2937.113 3177.333 2916.384 antibiogram of the strain. However, pulsed-field gel 2000 6548.995 6611.749 2000 electrophoresis (PFGE) and MLST for epidemiological The associated peaks in MRSA and MSSA: (Table 1) 1000 2900 2950 3000 3050 3100 3150 6400 6450 6500 6550 6600 6650 m /z m /z studies are is not suitable for clinical microbiology The 129 MRSA strains and 77 MSSA strains were directly prepared, Fig. 1：The related peaks of MRSA major clonal laboratories due to costly and labor-intensive.. introduced into mass spectrometry and performed mass spectrum analysis. We The flow process of identification of MLST type of MRSA clonal lineages: Recently, matrix-assisted laser desorption-time of flight could discriminate MRSA and MSSA by whether 2415, 2431, 2879 and 6593 We generalized the flow diagram for MLST identification by mass spectrum mass spectrometry (MALDI-TOF MS) has been utilized in m/z peaks are present or not. from these particular peaks (Fig. 2) and the predictive results. (Table 3) many clinical microbiology laboratories. It could not only Table 2: MRSA STs 5,45,59,239 clonal lineages associated peaks by MALDI TOF 3892 m/z identify bacterial species effectively and rapidly, but is an ST5 ( 28 isolates) ST45 ( 8 isolates) ST59 ( 27 isolates) ST239 ( 62 isolates) Yes No alternative solution for molecular methods. MS peaks (m/z) no. of isolate% of isolate no. of isolate% of isolate no. of isolate% of isolate no. of isolate% of isolate ST45, ST239 or ST59 Our purposes of this study were to discriminate MRSA and 3877 1 3.6 6 75 16 59.3 24 38.7 MSSA strain and identify the MRSA MLST type by protein 3892 15 53.6 0 0 0 0 0 0 3070 m/z mass fingerprints of MALDI-TOF MS analysis. 6552 28 100 8 100 26 96.3 19 30.6 No 6593 6 21.4 3 37.5 8 29.6 56 90.3 Yes Materials and Methods 3070 0 0 0 0 25 92.6 1 1.6 ST45 or ST239 Strain resource 3077 13 46.4 4 50 0 0 21 33.9 6593m/z The 206 strains of S. aureus, including 129 MRSA and 77 3084 1 3.6 0 0 17 63 2 3.2 MSSA, have been isolated from clinical blood samples since 4515 0 0 4 50 0 0 0 0 No Yes 4808 0 0 4 50 0 0 0 0 2009 to 2014 in Chung Gung Memorial hospital. ST45 or others Bacterial identification by MALDI-TOF MS 4515 or 4808 0 0 6 75 0 0 0 0 4515 or 4808 m/z The fresh bacterial colonies that grew on blood agar plate The related peaks of MRSA major clonal lineage ST5, ST45, ST59, and ST239 for 24 hours were picked and smeared onto a MALDI steel (Table 2, Fig. 1) No Yes target plate to thin films. 1 ul 70% formic acid were added We used MALDI-TOF MS to identify 125 known MRSA MLST sequence type for on films, dried at room temperature and following 1 ul comparison. As Table 2 and Fig. 1 shown, different MRSA STs have its unique matrix solution (50 % acetonitrite contain 1% α-cyano-4- peaks. To sum up, peaks at 3892 (ST5), 4515, 4808 (ST45), 6593(ST239), and 3070, hydroxycinnamic acid and 2.5% trifluoroacetic acid) were 3084 (ST59) m/z were each type’s specific signals. Fig. 2: Peak rules for MRSA major clonal lineages identification 4 then added on films again. Mass spectrum analysis was 110 0:F10 MS, Smoothed x10 4812.600 28 0:A10 MS Ra w 1400 1.5 Table 3: correct rate of MRSA clonal lineages identification 1200 Intens.[a.u.] Intens.[a.u.] 3890.988 MALDI BioTyper (Microflex; Bruker Daltonics) with linear 1000 ST5 ST5 1.0 no. of MRSA 800 4444.934 4589.021 0.5 positive model, and the analytic region was 2000-20000 Da. 600 4860.899 total no. ST5 ST59 ST239 ST45 other ST type 400 0.0 4 12 0:F6 MS, Smoothed x10 98 0:E2 MS Multilocus Sequence Typing (MLST) 1400 1.5 4807.630 129 28 27 62 8 4 1200 Intens.[a.u.] Intens.[a.u.] ST45 ST45 129 MRSA strains were sequenced for 7 housekeeping 1000 1.0 correct isolates no. 89 15 20 50 3 1 800 0.5 600 genes, including carbamate kinase , shikimate 4447.647 4592.054 4512.985 4861.445 400 correct rate (%) 69 53.5 74 80.6 37.5 25 0.0 x104 1400 16 0:E2 MS, Smoothed 16 0:E10 MS Ra w dehydrogenase, glycerol kinase , guanylate kinase , 1.5 1200 Intens.[a.u.] Intens.[a.u.] 1000 Conclusion ST59 1.0 ST59 4828.196 phosphate acetyltransferase , triosephosphate isomerase , 800 600 0.5 We could detect a part of MRSA early by analyzing the peaks of MALDI- 4446.313 and acetyl coenzyme A acetyltransferase genes. Sequencing 400 4845.032 200 0.0 4 22 0:E10 MS, Smoothed x10 2 0:A5 MS Ra w TOF MS and comprehend the MLST ST type whenever identifying bacterial 1400 3875.186 1.5 1200 Intens.[a.u.] results of these genes were compared to S. aureus MLST Intens.[a.u.] 4813.115 1000 strain in clinical microbiology laboratory. It is helpful to provide physicians ST239 1.0 ST239 database (http://asureus.mlst.net/) to acquire allelic number 800 600 4844.680 0.5 4445.690 for treatment information to patients and further investigation of 4589.707 400 and sequence type. 200 0.0 3800 3820 3840 3860 3880 3900 3920 3940 3960 3980 4400 4450 4500 4550 4600 4650 4700 4750 4800 4850 epidemiological outbreak. m /z m /z MRSA(129 isolates) MSSA(77 isolates) MS peaks (m/z) no. of isolate % of isolate no. of isolate % of isolate 2415 67 51.9 2 2.6 2431 65 50.4 0 0 2879 51 39.5 2 2.6 6593 77 59.7 7 9.1 Appear of any above peaks 103 79.8 11 14.3 none of above peaks 26 20.1 66 85.7.
Recommended publications
  • List of 246 Protein Complex Pairs Identified by DM-Align

    List of 246 Protein Complex Pairs Identified by DM-Align

    SUPPLEMENTARY MATERIAL Table S1: List of 246 protein complex pairs identified by DM-align. Query PDB IDa PDB Classb: Temp PDB IDd PDB Classb: TM- R(Å)f (Chain1,Chain2) GO termc (Chain1,Chain2) GO termc scoree 1djt (A,B) Toxin: Ion 1aap (A,B) Protease/Inhibitor 0.368 4.8 channel inhibitor complex: serine activity type endopeptidase activity and inhibitor 1dkf (A,B) Hormone/Growth 1xb7 (A1,A2) DNA binding and 0.849 3.1 Factor Receptor: Transcription DNA binding and factor activity transciption factor activity 1dl5 (A,B) Transferase: 1utx (A,B) DNA binding 0.437 3.9 Methyltransferas protein: Sequence e activity specific DNA binding 1dlf (L,H) Immunoglobin: 1j05 (L,H) Immunoglobin: 0.917 1.6 Antibody Antigen binding 1do5 (A,B) Chaperone: 1xso (A,B) Superoxide 0.953 0.9 Copper ion Acceptor: Copper binding activity ion binding 1dos (A,B) lyase: fructose- 1rvg (A,B) lyase: fructose- 0.760 3.6 biphosphate biphosphate aldolase aldolase 1dp4 (A,C) Hormone/Growth 1dz3 (A1,A2) Response 0.481 4.7 Factor Receptor: Regulator: DNA protein kinase binding and activity transcription factor activity 1dqp (A,B) Transferase: 1grv (A,B) Transferase: 0.856 2.9 transferring transferring glycosyl groups glycosyl groups 1dqw (A,B) Lyase: orotidin- 2jgy (A,B) Transferase: 0.95 1.7 5-phosphate orotidin-5- decarboxylase phosphate decarboxylase 1ds6 (A,B) Signalling 1cc0 (A,E) Signalling 0.897 2.2 Protein: GTPase Protein: GTPase activity activity 1dth (A,B) Hydrolase: 1sqv (A2,K2) Oxidoredutase: 0.423 2.7 Metaloendopepti Metaloendopepti dase activity dase activity 1dvf
  • The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose

    The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose

    Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota.
  • Saccharomyces Cerevisiae Aspartate Kinase Mechanism and Inhibition

    Saccharomyces Cerevisiae Aspartate Kinase Mechanism and Inhibition

    In compliance with the Canadian Privacy Legislation some supporting forms may have been removed from this dissertation. While these forms may be included in the document page count, their removal does not represent any loss of content from the dissertation. Ph.D. Thesis - D. Bareich McMaster University - Department of Biochemistry FUNGAL ASPARTATE KINASE MECHANISM AND INHIBITION By DAVID C. BAREICH, B.Sc. A Thesis Submitted to the School of Graduate Studies in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy McMaster University © Copyright by David C. Bareich, June 2003 1 Ph.D. Thesis - D. Bareich McMaster University - Department of Biochemistry FUNGAL ASPARTATE KINASE MECHANISM AND INHIBITION Ph.D. Thesis - D. Bareich McMaster University - Department of Biochemistry DOCTOR OF PHILOSOPHY (2003) McMaster University (Biochemistry) Hamilton, Ontario TITLE: Saccharomyces cerevisiae aspartate kinase mechanism and inhibition AUTHOR: David Christopher Bareich B.Sc. (University of Waterloo) SUPERVISOR: Professor Gerard D. Wright NUMBER OF PAGES: xix, 181 11 Ph.D. Thesis - D. Bareich McMaster University - Department of Biochemistry ABSTRACT Aspartate kinase (AK) from Saccharomyces cerevisiae (AKsc) catalyzes the first step in the aspartate pathway responsible for biosynthesis of L-threonine, L-isoleucine, and L-methionine in fungi. Little was known about amino acids important for AKsc substrate binding and catalysis. Hypotheses about important amino acids were tested using site directed mutagenesis to substitute these amino acids with others having different properties. Steady state kinetic parameters and pH titrations of the variant enzymes showed AKsc-K18 and H292 to be important for binding and catalysis. Little was known about how the S. cerevisiae aspartate pathway kinases, AKsc and homoserine kinase (HSKsc), catalyze the transfer of the y-phosphate from adenosine triphosphate (ATP) to L-aspartate or L-homoserine, respectively.
  • Supplementary Information

    Supplementary Information

    Supplementary information (a) (b) Figure S1. Resistant (a) and sensitive (b) gene scores plotted against subsystems involved in cell regulation. The small circles represent the individual hits and the large circles represent the mean of each subsystem. Each individual score signifies the mean of 12 trials – three biological and four technical. The p-value was calculated as a two-tailed t-test and significance was determined using the Benjamini-Hochberg procedure; false discovery rate was selected to be 0.1. Plots constructed using Pathway Tools, Omics Dashboard. Figure S2. Connectivity map displaying the predicted functional associations between the silver-resistant gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S3. Connectivity map displaying the predicted functional associations between the silver-sensitive gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S4. Metabolic overview of the pathways in Escherichia coli. The pathways involved in silver-resistance are coloured according to respective normalized score. Each individual score represents the mean of 12 trials – three biological and four technical. Amino acid – upward pointing triangle, carbohydrate – square, proteins – diamond, purines – vertical ellipse, cofactor – downward pointing triangle, tRNA – tee, and other – circle.
  • Q 297 Suppl USE

    Q 297 Suppl USE

    The following supplement accompanies the article Atlantic salmon raised with diets low in long-chain polyunsaturated n-3 fatty acids in freshwater have a Mycoplasma dominated gut microbiota at sea Yang Jin, Inga Leena Angell, Simen Rød Sandve, Lars Gustav Snipen, Yngvar Olsen, Knut Rudi* *Corresponding author: [email protected] Aquaculture Environment Interactions 11: 31–39 (2019) Table S1. Composition of high- and low LC-PUFA diets. Stage Fresh water Sea water Feed type High LC-PUFA Low LC-PUFA Fish oil Initial fish weight (g) 0.2 0.4 1 5 15 30 50 0.2 0.4 1 5 15 30 50 80 200 Feed size (mm) 0.6 0.9 1.3 1.7 2.2 2.8 3.5 0.6 0.9 1.3 1.7 2.2 2.8 3.5 3.5 4.9 North Atlantic fishmeal (%) 41 40 40 40 40 30 30 41 40 40 40 40 30 30 35 25 Plant meals (%) 46 45 45 42 40 49 48 46 45 45 42 40 49 48 39 46 Additives (%) 3.3 3.2 3.2 3.5 3.3 3.4 3.9 3.3 3.2 3.2 3.5 3.3 3.4 3.9 2.6 3.3 North Atlantic fish oil (%) 9.9 12 12 15 16 17 18 0 0 0 0 0 1.2 1.2 23 26 Linseed oil (%) 0 0 0 0 0 0 0 6.8 8.1 8.1 9.7 11 10 11 0 0 Palm oil (%) 0 0 0 0 0 0 0 3.2 3.8 3.8 5.4 5.9 5.8 5.9 0 0 Protein (%) 56 55 55 51 49 47 47 56 55 55 51 49 47 47 44 41 Fat (%) 16 18 18 21 22 22 22 16 18 18 21 22 22 22 28 31 EPA+DHA (% diet) 2.2 2.4 2.4 2.9 3.1 3.1 3.1 0.7 0.7 0.7 0.7 0.7 0.7 0.7 4 4.2 Table S2.
  • Product Information Sheet for NR-19577

    Product Information Sheet for NR-19577

    Product Information Sheet for NR-19577 Streptococcus pneumoniae Gateway® Packaging/Storage: Clone Set, Recombinant in Escherichia NR-19577 was packaged aseptically in a 96-well plate. The product is provided frozen and should be stored at -80°C or coli, Plate 10 colder immediately upon arrival. For long-term storage, the vapor phase of a liquid nitrogen freezer is recommended. Catalog No. NR-19577 Freeze-thaw cycles should be avoided. This reagent is the tangible property of the U.S. Government. Growth Conditions: For research use only. Not for human use. Media: LB broth containing 50 µg/mL kanamycin LB agar containing 50 µg/mL kanamycin Contributor: Incubation: Pathogen Functional Genomics Resource Center at the J. Temperature: 37°C Craig Venter Institute Atmosphere: Aerobic Propagation: Manufacturer: 1. Scrape top of frozen well with a pipette tip and streak BEI Resources onto agar plate. 2. Incubate the plates at 37°C for 18 to 24 hours. Product Description: Clone plates are replicated using a BioMek® FX robot. Citation: Production in the 96-well format has increased risk of cross- Acknowledgment for publications should read “The following contamination between adjacent wells. Individual clones reagent was obtained through BEI Resources, NIAID, NIH: should be purified (e.g. single colony isolation and Streptococcus pneumoniae Gateway® Clone Set, purification using good microbiological practices) and Recombinant in Escherichia coli, Plate 10, NR-19577.” sequence-verified prior to use. BEI Resources only confirms the clone plate orientation and viability of randomly picked Biosafety Level: 1 clones. BEI Resources does not confirm or validate Appropriate safety procedures should always be used with individual clone identities provided by the contributor.
  • Consolidated List of Up-Regulated Proteins Expressed at Different Cr (VI) Concentrations at Time Points

    Consolidated List of Up-Regulated Proteins Expressed at Different Cr (VI) Concentrations at Time Points

    Electronic Supplementary Material (ESI) for Metallomics.
  • Grasnotice 946, Lactobacillus Plantarum Strain DSM 33452

    Grasnotice 946, Lactobacillus Plantarum Strain DSM 33452

    GRAS Notice (GRN) No. 946 https://www.fda.gov/food/generally-recognized-safe-gras/ RECEIVED gras-notice-inventory JUNO 2 1020 Chr. Hansen, In -?FFICE OF FOOD ADD ITIVE SAFETY 9015 West Maple Street Milwaukee, WI 53214 - 4298 Division of Biotechnology and GRAS Notice Review U.S .A. Center for Food Safety & Applied Nutrition (HFS-255) U.S. Food & Drug Administration Phone 414 - 607 - 5700 Fax 414 - 607 - 5959 Reference: Lactobacillus plantarum DSM 33452 June 1, 2020 Dear Sir or Madam, In accordance with the Federal Register [81 Fed. Reg. 159 (17 August 2016)] issuance on Generally Recognized as Safe (GRAS) notifications (21 CFR Part 170), Chr. Hansen is pleased to submit a notice that we have concluded, through scientific procedures that Lactobacillus plantarum (L. plantarum) DSM 33452 is generally recognized as safe for use in malolactic fermentation of wine and musts and is not subject to the pre-market approval requirements. The recommendation is to inoculate the pure starter culture of L. plantarum DSM 33452 into wine or must at an inoculation level of 1.0E+07 CFU/g at the time of crushing grapes or as early as possible in the fermentation tanks. L. plantarum DSM 33452 is sensitive to alcohol concentration, so the concentration of the organism will decrease as the concentration of alcohol in the wine or must increases. Though L. plantarum DSM 33452 is safe to consume, it would be present at negligible levels, if at all, in the finished product. It should also be noted that due to recent taxonomic changes to the genus Lactobaci/lus, Lactobacillus plantarum will be known as Lactiplantibacillus plantarum moving forward (Zheng, et al., 2020).
  • Assay for Detecting Mycoplasma by Measuring Acetate Kinase Or Carbamate Kinase Activity

    Assay for Detecting Mycoplasma by Measuring Acetate Kinase Or Carbamate Kinase Activity

    (19) & (11) EP 2 264 181 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 22.12.2010 Bulletin 2010/51 C12Q 1/04 (2006.01) C12Q 1/48 (2006.01) C12Q 1/00 (2006.01) (21) Application number: 10075423.3 (22) Date of filing: 16.04.2004 (84) Designated Contracting States: • Crouch, Sharon Patricia Mary AT BE BG CH CY CZ DE DK EE ES FI FR GB GR Nottingham NG7 1DQ (GB) HU IE IT LI LU MC NL PL PT RO SE SI SK TR • Slater, Kevin John Nottingham NG7 1ED (GB) (30) Priority: 17.04.2003 GB 0308829 • Cox, Anne 17.04.2003 US 436323 P Long Eaton, Nottingham NG10 3JB (GB) (62) Document number(s) of the earlier application(s) in (74) Representative: Didmon, Mark et al accordance with Art. 76 EPC: Potter Clarkson LLP 04727944.3 / 1 613 763 Park View House 58 The Ropewalk (71) Applicant: Cambrex Bio Science Nottingham Nottingham NG1 5DD (GB) Limited Nottingham NG1 1GF (GB) Remarks: This application was filed on 13-09-2010 as a (72) Inventors: divisional application to the application mentioned • Pitt, Anthony under INID code 62. Beeston, Nottingham NG9 2BE (GB) (54) ASSAY FOR DETECTING MYCOPLASMA BY MEASURING ACETATE KINASE OR CARBAMATE KINASE ACTIVITY (57) The invention relates to a method of detecting (ii) detecting and/or measuring the activity of acetate ki- the presence of mycoplasma in a test sample comprising: nase and/or carbamate kinase in the test sample, the (i) providing a test sample; and activity being indicative of contamination by mycoplas- ma.
  • The Carbamate Kinase-Like Carbamoyl Phosphate Synthetase of The

    The Carbamate Kinase-Like Carbamoyl Phosphate Synthetase of The

    Proc. Natl. Acad. Sci. USA Vol. 94, pp. 12803–12808, November 1997 Biochemistry The carbamate kinase-like carbamoyl phosphate synthetase of the hyperthermophilic archaeon Pyrococcus furiosus, a missing link in the evolution of carbamoyl phosphate biosynthesis VIRGINIE DURBECQ*, CHRISTIANNE LEGRAIN†,MARTINE ROOVERS‡§,ANDRE´ PIE´RARD*†, AND NICOLAS GLANSDORFF†‡§¶ *Laboratoire de Microbiologie, Universite´Libre de Bruxelles, †Research Institute of the Centre de Recherches et d’Enseignement des Industries Alimentaires et Chimiques, ‡Microbiologie, Vrije Universiteit Brussel, and §Flanders Interuniversity Institute for Biotechnology, Avenue E. Gryson 1, B-1070 Brussels, Belgium Communicated by H. Edwin Umbarger, Purdue University, West Lafayette, IN, September 16, 1997 (received for review July 9, 1997) ABSTRACT Microbial carbamoyl phosphate synthetases protein, and it was proposed that the synthetase gene had (CPS) use glutamine as nitrogen donor and are composed of evolved by duplication of a smaller ancestral gene—possibly two subunits (or domains), one exhibiting glutaminase activ- coding for a carbamate kinase (CK) (5). CKs (EC 2.7.2.2) are ity, the other able to synthesize carbamoyl phosphate (CP) homodimers composed of subunits of 31–37 kDa (6). As from bicarbonate, ATP, and ammonia. The pseudodimeric carbamate is in chemical equilibrium with bicarbonate and 2 organization of this synthetase suggested that it has evolved by ammonia, CK can synthesize CP from HCO3 ,NH3 and one duplication of a smaller kinase, possibly a carbamate kinase molecule of ATP (Fig. 1). This evolutionary scheme found (CK). In contrast to other prokaryotes the hyperthermophilic support in the weak but nevertheless suggestive sequence archaeon Pyrococcus furiosus was found to synthesize CP by similarities that were brought to light between carB and the using ammonia and not glutamine.

  • Sigma Enzymes, Coenzymes and Enzyme Substrates

    Sigma Enzymes, Coenzymes and Enzyme Substrates Library Listing – 485 spectra This library represents a material-specific subset of the larger Sigma Biochemical Condensed Phase Library relating to enzymes, coenzymes and enzyme substrates found in the Sigma Biochemicals and Reagents catalog. Spectra acquired by Sigma-Aldrich Co. which were examined and processed at Thermo Fisher Scientific. The spectra include compound name, molecular formula, CAS (Chemical Abstract Service) registry number, and Sigma catalog number. Sigma Enzymes, Coenzymes and Enzyme Substrates Index Compound Name Index Compound Name 484 (E)-Vaccenoyl coenzyme A 298 Azo soybean flour 483 (Z)-Vaccenoyl coenzyme A 295 Azoalbumin 400 1,N6-Etheno acetyl coenzyme A, Li salt 296 Azocasein 401 1,N6-Etheno coenzyme A, Na + Li salt 297 Azocoll 397 11,14,17-Eicosatrienoyl coenzyme A 379 Behenoyl coenzyme A 396 11,14-Eicosadienoyl coenzyme A 380 Benzoyl coenzyme A, Li salt 395 11-Eicosaenoyl coenzyme A 343 Bis-(p-nitrophenyl) phosphate 321 2-(b-D-Galactosidoxy)naphthol AS-LC 344 Bis-(p-nitrophenyl) phosphate, Ca salt 394 3'-Dephosphocoenzyme A 345 Bis-(p-nitrophenyl) phosphate, Na salt 370 3-Acetylpyridine adenine dinucleotide 381 Brassidoyl coenzyme A 372 3-Acetylpyridine adenine dinucleotide 9 Carbamate kinase from streptococcus phosphate, Na salt faecalis 371 3-Acetylpyridine adenine dinucleotide, 310 Carbamyl phosphate, diammonium salt reduced form 311 Carbamyl phosphate, dilithium salt 373 3-Acetylpyridine-hypoxanthine 312 Carbamyl phosphate, disodium salt dinucleotide 10 Carbonic

  • BMC Structural Biology Biomed Central

    BMC Structural Biology BioMed Central Research article Open Access A comprehensive update of the sequence and structure classification of kinases Sara Cheek2, Krzysztof Ginalski2,3, Hong Zhang2 and Nick V Grishin*1,2 Address: 1Howard Hughes Medical Institute, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA, 2Department of Biochemistry, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA and 3Bioinformatics Laboratory, Interdisciplinary Centre for Mathematical and Computational Modelling Warsaw University, Pawinskiego 5a, 02-106 Warsaw, Poland Email: Sara Cheek - [email protected]; Krzysztof Ginalski - [email protected]; Hong Zhang - [email protected]; Nick V Grishin* - [email protected] * Corresponding author Published: 16 March 2005 Received: 11 January 2005 Accepted: 16 March 2005 BMC Structural Biology 2005, 5:6 doi:10.1186/1472-6807-5-6 This article is available from: http://www.biomedcentral.com/1472-6807/5/6 © 2005 Cheek et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: A comprehensive update of the classification of all available kinases was carried out. This survey presents a complete global picture of this large functional class of proteins and confirms the soundness of our initial kinase classification scheme. Results: The new survey found the total number of kinase sequences in the protein database has increased more than three-fold (from 17,310 to 59,402), and the number of determined kinase structures increased two-fold (from 359 to 702) in the past three years.