PCR of the Human Mitochondrial Segment Encoding for Trna Glycine (Bp 10,009 to 10,216)

Total Page:16

File Type:pdf, Size:1020Kb

PCR of the Human Mitochondrial Segment Encoding for Trna Glycine (Bp 10,009 to 10,216) PFU DNA Polymerase: A Study of Amplification Error Rate and Subsequent Implications for High Fidelity Mutational Spectrometry by Sheila Gay Buzzee B.S. Biology, Xavier University December, 1989 Submitted to the Department of Civil and Environmental Engineering in partial fulfillment of the requirements for the degree of Master of Science in Civil and Environmental Engineering at the MASSACHUSETTS INSTITUTE OF TECHNOLOGY January 1994 Copyright by the Massachusetts Institute of Technology 1994. All rights reserved. Author........ .............................. Department of Cl andonmental Engineering January 26, 1994 C ertified by.....................:.-.................................,............................ .... William Thilly, Professor of Toxicology Professor of Civil and Environmental Engineering n Thesis Supervisor Accepted by ..................... ................... ................................. Professor Joseph Sussman Chairman, Department Committee on Graduate Students PFU DNA Polymerase: A Study of Amplification Error Rate and Subsequent Implications for High Fidelity Mutational Spectrometry by Sheila Gay Buzzee Submitted to the Department of Civil and Environmental Engineering on January 26, 1994, in partial fulfillment of the requirements for the degree of Master of Science in Civil and Environmental Engineering. Abstract This thesis tested the Pyrococcus furiosus (PFU) thermostabile DNA polymerase during PCR of the human mitochondrial segment encoding for tRNA glycine (bp 10,009 to 10,216). This segment is of particular interest for highly precise human mutational spectrometry studies, and the enzyme was tested to determine what amplification error rate may be anticipated in this application, and what the implications are for future human mutational studies. The enzyme was tested under conditions in which cellular DNA was amplified through 20, 40, and 60 sequential doublings so that the enzyme error rate could be determined along a wide curve. The enzyme was tested in tandem with Tli (VentTM) DNA polymerase for control purposes and error rate comparison. The enzyme was tested under standard laboratory use conditions, and tested additionally in conditions designed to fully extend incomplete extension products, hypothesized to account for a significant portion of observable background noise during mutational spectrometry using gel electrophoresis. As was previously reported by Lundberg et al [20], PFU DNA polymerase was found under standard laboratory practice to have an error rate lower than Tli (VentTM) DNA polymerase. The observed error rate is no more than 1.6 x 106 errors per base pair duplication. Furthermore this error rate was observed to be significantly reduced by additional DNA treatment to fully extend incomplete extension products. This additional treatment consisted of purification of PCR product, resuspension of the DNA, and preparation of a reaction mixture which mimics the PCR recipe but is lacking primers. This new reaction is thermocycled in the presence of PFU DNA polymerase under identical temperature conditions as PCR. This procedure allows for the complete extension of all DNA in the reaction mixture, but some DNA degradation occurs due to the high exonuclease activity of PFU. Thesis Supervisor: William G. Thilly Title: Professor of Toxicology, Professor of Civil and Environmental Engineering Acknowledgments I offer my sincere thanks and profound gratitude to Dr. John Hanekamp for his consistent support, advice, technical assistance, and unfailing friendship. Thanks also to Riitta and Jia, my wonderfully supportive and sympathetic office mates, to Hilary for keeping me company in lab at even the latest of hours, to Dr. Konstantin Khrapko and Dr. Gengxi Hu for advice, hints when I felt stuck, and sincere encouragement, and to Mark and Paula and Paulo and Aoy and all the other friendly faces for helping me keep my sense of humor no matter how tired I got. Thanks in particular to Professor Thilly for providing me with a unique environment for learning, and a forum of collaborators to discuss and experiment and create the future for ourselves. I wish you and your scientific melting pot many years of fruitful research. Thanks most importantly to my private fans and supporters- you will never know how much your encouragement has fueled me and fed me as I struggled through the long hours and (seeming) technical impossibilities. Thanks to you all, in no particular order: Mom, Dad, Sarah, Nancy, Stefan, Sarah S., Jamie, The Friday Lunch Bunch, Pat and Brian, and Ken and Jen. Contents 1 Introduction 9 2 Literature Overview 11 2.1 Mutational Spectrometry 11 2.2 Denaturing Gel Electrophoresis 11 2.2.1 Denaturing Gradient Gel Electrophoresis 11 (DGGE) 2.2.2 Constant Denaturant Capillary Electrophoresis 13 (CDCE) 2.3 Polymerase Chain Reaction (PCR) 13 2.3.1 Thermostabile Enzymes and Enzyme Fidelity 14 2.3.2 Enzyme Efficiency 15 2.4 Pyrococcusfuriosus(PFU) DNA Polymerase 16 3 Materials and Methods 17 3.1 DNA Isolation 17 3.2 Polymerase Chain Reaction 18 3.2.1 Standard PCR Procedure and Sequential 19 Amplification 3.2.2 Additional Extension Procedure 21 3.3 DNA Purification 22 3.3.1 Gel Electrophoresis 22 3.3.2 DNA Elution 22 3.4 Denaturation and Rehybridization 23 3.5 DNA Analysis 23 3.5.1 DGGE Technique 23 3.5.2 CDCE Technique 24 3.5.3 Quantification of Noise 25 4 Results 26 4.1 Sequential DNA Amplification 26 4.2 DGGE Sample Analysis 29 4.3 CDCE Sample Analysis 32 4.4 Phosphorimager Quantification of Noise 32 5 Discussion 38 5.1 Sequential Amplification 38 5.2 PFU Noise Evaluation 39 6 Conclusions 40 6.1 Direct Implications 40 6.2 Areas for Future Study 41 Bibliography 43 List of Figures 4. la PAGE visualization of first PFU amplification 28 4. lb PAGE visualization of second round of PFU amplification 28 4.1 c PAGE visualization of third round of PFU amplification 28 4. Id PAGE visualization of fourth round of PFU amplification 28 4. l1e PAGE visualization of fifth round of PFU amplification 28 4.2 DGGE of Tli VentTM versus PFU, 20 duplications 30 4.3 DGGE of PFU 20, 40, and 60 duplications 30 4.4 DGGE of terminal extension cycling and unaltered product, 31 20 duplications 4.5 CDCE of PFU amplified DNA 33 4.6 CDCE of PFU amplified multiple ss peaks 34 4.7 Phosphor scan of PFU versus Tli VentTM amplified DNA 36 4.8 Phosphor scan of terminal extension and unaltered product, 37 20 duplications List of Tables 2.1 Reported enzyme fidelities 15 3.1 PCR reaction recipe: Tli VentTM, PFU, PFU as per Lundberg et al [20] 20 4. la PCR results, first amplification 26 4. lb PCR sequential amplification, round two results 27 4. Ic PCR sequential amplification, round three results 27 4. Id PCR sequential amplification, round four results 29 4. le PCR sequential amplification, round five results 29 4.2 PFU and Tli VentTM fidelity quantification by phosphor scan 35 List of Abbreviations bp base pair(s) BSA bovine albumin serum CDCE constant denaturant capillary electrophoresis DGGE denaturing gradient gel electrophoresis dNTP deoxyribonucleoside triphosphate EtdBr ethidium bromide EtOH ethyl alcohol f enzyme fidelity HeF heteroduplex fraction hmd high melting domain lmd low melting domain MOPS 3(N-morpholino)propanesulfonic acid nt Nucleotide(s) PAGE polyacrylamide gel electrophoresis PCR polymerase chain reaction PFU DNA polymerase obtained from Pyrococcusfuriosus rpm revolutions per minute ss single stranded TAE 40mM Tris-acetate, ImM EDTA (pH = 8.0 at 25 0 C) TBE 45mM Tris-borate, ImM EDTA (pH = 8.0 at 25 0 C) TEMED N,N,N',N'-tetramethylethylenediamine UV ultraviolet WT wild type Chapter 1 Introduction Mutational spectrometry is the science of determining unique and reproducible mutant patterns in DNA, and of characterizing both qualitatively and quantitatively the nature of those mutations. [1, 4 ,21, 27, 28, 29] In order to observe rare, low frequency mutants and avoid working with very large numbers of cells, it is necessary to amplify DNA for study using the polymerase chain reaction (PCR). [16, 24] Polymerase enzyme fidelity, f, is of obvious importance to mutational spectrometry- an enzyme which has poor fidelity will introduce false signals into the system. Incorrectly amplified sequences, if present in levels comparable to the expected mutant fraction, will be indistinguishable from actual mutants and may mask mutant signals altogether. This thesis tested the Pyrococcus furiosus (PFU) thermostabile DNA polymerase during PCR of the human mitochondrial segment encoding for tRNA glycine (bp 10,009 to 10,216). This multicopy segment is of particular interest for highly precise human mutational spectrometry studies, and the enzyme was tested to determine what amplification error rate may be anticipated in this application, and what the subsequent implications are for future human mutational studies. This enzyme has been reported previously to have a very high fidelity, 1.6 x 10-6 errors per base pair duplication, in a study of DNA amplification, cloning, and plating for mutant colonies. [20] Cloning is less precise than electrophoretic mutational spectroscopy and may contain internal bias in situations of inadequate sample size. Additionally the methods utilized by Lundberg et al include resin binding to remove polymerase activity and DNA eleution; both have the potential to induce mutations in DNA [10, 20]. As the enzyme fidelity reported by Lundberg is the highest of any thermostabile enzyme described to date, PFU DNA polymerase was deemed potentially very important to electrophoretic mutational
Recommended publications
  • A Proposal to Rename the Hyperthermophile Pyrococcus Woesei As Pyrococcus Furiosus Subsp
    Archaea 1, 277–283 © 2004 Heron Publishing—Victoria, Canada A proposal to rename the hyperthermophile Pyrococcus woesei as Pyrococcus furiosus subsp. woesei WIROJNE KANOKSILAPATHAM,1 JUAN M. GONZÁLEZ,1,2 DENNIS L. MAEDER,1 1,3 1,4 JOCELYNE DIRUGGIERO and FRANK T. ROBB 1 Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, MD 21202, USA 2 Present address: IRNAS-CSIC, P.O. Box 1052, 41080 Sevilla, Spain 3 Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20274, USA 4 Corresponding author ([email protected]) Received April 8, 2004; accepted July 28, 2004; published online August 31, 2004 Summary Pyrococcus species are hyperthermophilic mem- relatively rapidly at temperatures above 90 °C and produce ° bers of the order Thermococcales, with optimal growth tem- H2S from elemental sulfur (S ) (Zillig et al. 1987). Two Pyro- peratures approaching 100 °C. All species grow heterotrophic- coccus species, P. furiosus (Fiala and Stetter 1986) and ° ally and produce H2 or, in the presence of elemental sulfur (S ), P. woesei (Zillig et al. 1987), were isolated from marine sedi- H2S. Pyrococcus woesei and P.furiosus were isolated from ma- ments at a Vulcano Island beach site in Italy. They have similar rine sediments at the same Vulcano Island beach site and share morphological and physiological characteristics: both species many morphological and physiological characteristics. We re- are cocci and move by means of a tuft of polar flagella. They port here that the rDNA operons of these strains have identical are heterotrophic and grow optimally at 95–100 °C, utilizing sequences, including their intergenic spacer regions and part of peptides as major carbon and nitrogen sources.
    [Show full text]
  • High-Fidelity Amplification Using a Thermostable DNA Polymerase Isolated from P’~Ococcusfuriosus
    Gette, 108 (1991) 1-6 8 1991 Elsevier Science Publishers B.V. All rights reserved. 0378-l 119/91/SO3.50 GENE 06172 High-fidelity amplification using a thermostable DNA polymerase isolated from P’~OCOCCUSfuriosus (Polymerase chain reaction; mutation frequency; lack; proofreading; 3’40-5 exonuclease; recombinant DNA; archaebacteria) Kelly S. Lundberg”, Dan D. Shoemaker*, Michael W.W. Adamsb, Jay M. Short”, Joseph A. Serge* and Eric J. Mathur” “ Division of Research and Development, Stratagene, Inc., La Jolla, CA 92037 (U.S.A.), and h Centerfor Metalloen~~vme Studies, University of Georgia, Athens, GA 30602 (U.S.A.) Tel. (404/542-2060 Received by M. Salas: 16 May 1991 Revised/Accepted: 11 August/l3 August 1991 Received at publishers: 17 September 1991 -.-- SUMMARY A thermostable DNA polymerase which possesses an associated 3’-to-5’ exonuclease (proofreading) activity has been isolated from the hyperthermophilic archaebacterium, Pyrococcus furiosus (Pfu). To test its fidelity, we have utilized a genetic assay that directly measures DNA polymerase fidelity in vitro during the polymerase chain reaction (PCR). Our results indicate that PCR performed with the DNA polymerase purified from P. furiosus yields amplification products containing less than 10s.~ of the number of mutations obtained from similar amplifications performed with Tuq DNA polymerase. The PCR fidelity assay is based on the ampli~cation and cloning of lad, lac0 and IacZor gene sequences (IcrcIOZa) using either ffil or 7ii~irqDNA poIymerase. Certain mutations within the lucf gene inactivate the Lac repressor protein and permit the expression of /?Gal. When plated on a chromogenic substrate, these Lacl - mutants exhibit a blue-plaque phenotype.
    [Show full text]
  • Tackling the Methanopyrus Kandleri Paradox Céline Brochier*, Patrick Forterre† and Simonetta Gribaldo†
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Open Access Research2004BrochieretVolume al. 5, Issue 3, Article R17 Archaeal phylogeny based on proteins of the transcription and comment translation machineries: tackling the Methanopyrus kandleri paradox Céline Brochier*, Patrick Forterre† and Simonetta Gribaldo† Addresses: *Equipe Phylogénomique, Université Aix-Marseille I, Centre Saint-Charles, 13331 Marseille Cedex 3, France. †Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris-Sud, 91405 Orsay, France. reviews Correspondence: Céline Brochier. E-mail: [email protected] Published: 26 February 2004 Received: 14 November 2003 Revised: 5 January 2004 Genome Biology 2004, 5:R17 Accepted: 21 January 2004 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2004/5/3/R17 reports © 2004 Brochier et al.; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. ArchaealPhylogeneticsequencedusingrespectively). two phylogeny concatenated genomes, analysis based it of is datasetsthe now on Archaea proteinspossible consisting has ofto been thetest of transcription alternative mainly14 proteins established approach involv and translationed byes in 16S bytranscription rRNAusing machineries: largesequence andsequence 53comparison.tackling ribosomal datasets. the Methanopyrus Withproteins We theanalyzed accumulation(3,275 archaealkandleri and 6,377 of phyparadox comp positions,logenyletely Abstract deposited research Background: Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets.
    [Show full text]
  • Comparative Genomic Analysis of The
    de Crécy-Lagard et al. Biology Direct 2012, 7:32 http://www.biology-direct.com/content/7/1/32 RESEARCH Open Access Comparative genomic analysis of the DUF71/ COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage Valérie de Crécy-Lagard1*, Farhad Forouhar2, Céline Brochier-Armanet3, Liang Tong2 and John F Hunt2 Abstract Background: The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with function by genetic or biochemical approaches, a lengthy process that often took years. Phylogenetic distribution profiles, physical clustering, gene fusion, co-expression profiles, structural information and other genomic or post-genomic derived associations can be now used to make very strong functional hypotheses. Here, we illustrate this shift with the analysis of the DUF71/COG2102 family, a subgroup of the PP-loop ATPase family. Results: The DUF71 family contains at least two subfamilies, one of which was predicted to be the missing diphthine-ammonia ligase (EC 6.3.1.14), Dph6. This enzyme catalyzes the last ATP-dependent step in the synthesis of diphthamide, a complex modification of Elongation Factor 2 that can be ADP-ribosylated by bacterial toxins. Dph6 orthologs are found in nearly all sequenced Archaea and Eucarya, as expected from the distribution of the diphthamide modification. The DUF71 family appears to have originated in the Archaea/Eucarya ancestor and to have been subsequently horizontally transferred to Bacteria. Bacterial DUF71 members likely acquired a different function because the diphthamide modification is absent in this Domain of Life.
    [Show full text]
  • Purification and Properties of Extracellular Amylase from The
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Apr. 1995, p. 1502–1506 Vol. 61, No. 4 0099-2240/95/$04.0010 Copyright q 1995, American Society for Microbiology Purification and Properties of Extracellular Amylase from the Hyperthermophilic Archaeon Thermococcus profundus DT5432 YOUNG CHUL CHUNG, TETSUO KOBAYASHI,* HARUHIKO KANAI, TERUHIKO AKIBA, AND TOSHIAKI KUDO Laboratory of Microbiology, The Institute of Physical and Chemical Research (RIKEN), 2-1 Hirosawa, Wako, Saitama 351-01, Japan Received 22 September 1994/Accepted 13 January 1995 A hyperthermophilic archaeon, Thermococcus profundus DT5432, produced extracellular thermostable amy- lases. One of the amylases (amylase S) was purified to homogeneity by ammonium sulfate precipitation, DEAE-Toyopearl chromatography, and gel filtration on Superdex 200HR. The molecular weight of the enzyme was estimated to be 42,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The amylase exhib- ited maximal activity at pH 5.5 to 6.0 and was stable in the range of pH 5.9 to 9.8. The optimum temperature for the activity was 80&C. Half-life of the enzyme was3hat80&C and 15 min at 90&C. Thermostability of the enzyme was enhanced in the presence of 5 mM Ca21 or 0.5% soluble starch at temperatures above 80&C. The enzyme activity was inhibited in the presence of 5 mM iodoacetic acid or 1 mM N-bromosuccinimide, suggest- ing that cysteine and tryptophan residues play an important role in the catalytic action. The amylase hydro- lyzed soluble starch, amylose, amylopectin, and glycogen to produce maltose and maltotriose of a-configura- tion as the main products. Smaller amounts of larger maltooligosaccharides were also produced with a trace amount of glucose.
    [Show full text]
  • Pyrococcus Furiosus
    Mechanism of oxygen detoxification by the surprisingly oxygen-tolerant hyperthermophilic archaeon, Pyrococcus furiosus Michael P. Thorgersen, Karen Stirrett, Robert A. Scott, and Michael W. W. Adams1 Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 Edited by Douglas C. Rees, Howard Hughes Medical Institute, Caltech, Pasadena, CA, and approved September 27, 2012 (received for review May 21, 2012) The anaerobic archaeon Pyrococcus furiosus grows by fermenting In general, anaerobic organisms lack the classical defense mech- carbohydrates producing H2,CO2, and acetate. We show here that anism against reactive oxygen species (ROS) found in aerobic it is surprisingly tolerant to oxygen, growing well in the presence organisms, which includes superoxide dismutase and catalase, of 8% (vol/vol) O2. Although cell growth and acetate production although there are some exceptions (8–10). This is the case for were not significantly affected by O2,H2 production was reduced P. furiosus because its genome contains no homologs of either of by 50% (using 8% O2). The amount of H2 produced decreased in a these enzymes (11). In contrast, anaerobes have been proposed to linear manner with increasing concentrations of O2 over the range contain a superoxide-reducing system based on superoxide re- – 2 12% (vol/vol), and for each mole of O2 consumed, the amount of ductase (SOR), an enzyme first identified in P. furiosus (12). An H2 produced decreased by approximately 2 mol. The recycling of SOR homolog from Desulfoarculus baarsii was first implicated in − H2 by the two cytoplasmic hydrogenases appeared not to play a dealing with superoxide (O2 ) when it was able to suppress the role in O2 resistance because a mutant strain lacking both enzymes phenotypes of an E.
    [Show full text]
  • Archaeon Methanococcus Voltae JORDAN KONISKY,* SUZANNE M
    JOURNAL OF BACrERIOLOGY, Oct. 1994, p. 6402-6403 Vol. 176, No. 20 0021-9193/94/$04.00+0 Copyright © 1994, American Society for Microbiology The DNA Polymerase Gene from the Methanogenic Archaeon Methanococcus voltae JORDAN KONISKY,* SUZANNE M. PAULE, MARIA E. CARINATO, AND JANICE W. KANSY Department ofMicrobiology, University of Illinois, Urbana, Illinois 61801 Received 23 June 1994/Accepted 16 August 1994 Previous studies have identified intervening sequences that encode homing endonucleases within the genes encoding several archaeal DNA polymerases. We report the sequence of the gene encoding the DNA polymerase of Methanococcus voltae and describe evidence that it lacks analogous intervening sequences. Recent studies have identified the presence of in-frame littoralis DNA polymerases (1,311 and 1,702 amino acids, insertions in the structural genes encoding the DNA poly- respectively), the lengths of the mature forms of these poly- merases of the archaeon Thermococcus littoralis (7, 10) and merases are more similar (775 and 774 amino acids, respec- Pyrococcus species strain GB-D (17). In both cases, the pri- tively) to that of the M. voltae translation product. Multiple- mary translation product is processed to yield an internal alignment analysis of the amino acid sequences derived for the protein(s) (termed the intein[s] [11]) and the active mature mature forms of the Pyrococcus species strain GB-D and T. protein formed by the joining of the external sequences littoralis enzymes and the presumptive primary translation (termed the extein [11]). Similar protein-splicing events have products of the M. voltae, Sulfolobus solfataricus (882 amino been described for the production of the mature 69-kDa acids [12]), and P.
    [Show full text]
  • Downloaded (July 2018) and Aligned Using Msaprobs V0.9.7 (16)
    bioRxiv preprint doi: https://doi.org/10.1101/524215; this version posted January 20, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Positively twisted: The complex evolutionary history of Reverse Gyrase suggests a non- hyperthermophilic Last Universal Common Ancestor Ryan Catchpole1,2 and Patrick Forterre1,2 1Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Département de Microbiologie F-75015 Paris, France 2Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France 1 bioRxiv preprint doi: https://doi.org/10.1101/524215; this version posted January 20, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract Reverse gyrase (RG) is the only protein found ubiquitously in hyperthermophilic organisms, but absent from mesophiles. As such, its simple presence or absence allows us to deduce information about the optimal growth temperature of long-extinct organisms, even as far as the last universal common ancestor of extant life (LUCA). The growth environment and gene content of the LUCA has long been a source of debate in which RG often features. In an attempt to settle this debate, we carried out an exhaustive search for RG proteins, generating the largest RG dataset to date.
    [Show full text]
  • The Structure of Pyrococcus Furiosus Glutamate Dehydrogenase Reveals
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures KSP Yip', TJ Stillman', KL Britton1 , PJ Artymiuk', PJ Baker'1, SE Sedelnikova1, PC Engel' t, A Pasquo2 , R Chiaraluce2 , V Consalvi2, R Scandurra2 and DW Rice1* 1 The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, PO Box 594, Sheffield S10 2UH, UK and 2 Dipartimento di Scienze Biochimiche, Universita La Sapienza, Roma 00185, Italy Background: The hyperthermophile Pyrococcusfuriosus is glutamate dehydrogenase from the mesophile Clostridium one of the most thermostable organisms known, with symbiosum. an optimum growth temperature of 1000C. The proteins Conclusions: Comparison of the structures of these two from this organism display extreme thermostability. We enzymes has revealed one major difference: the structure have undertaken the structure determination of glutamate of the hyperthermophilic enzyme contains a striking series dehydrogenase from P. furiosus in order to gain further of ion-pair networks on the surface of the protein insights into the relationship between molecular structure subunits and buried at both interdomain and inter- and thermal stability. subunit interfaces. We propose that the formation of such Results: The structure of P. furiosus glutamate dehydro- extended networks
    [Show full text]
  • A Simple Method for In-House Pfu DNA Polymerase Purification for High
    Volume 11 Number 2 (April 2019) 181-186 A simple method for in-house Pfu DNA polymerase purification for high-fidelity PCR amplification TICLE R A Prabu Siva Sankar1, Marimuthu Citartan1*, Aminah Ahmed Siti1, Boris V. Skryabin2, 2 3 1 Timofey S. Rozhdestvensky , Goot Heah Khor , Thean Hock Tang ORIGINAL 1Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, Kepala Batas, Penang, Malaysia 2Medical Faculty (TRAM), University of Muenster, Muenster, Germany 3Centre of Preclinical Science Studies, Faculty of Dentistry, Universiti Teknologi MARA, Sungai Buluh Campus, Selangor, Malaysia Received: October 2018, Accepted: January 2019 ABSTRACT Background and Objectives: Pfu DNA polymerase is an enzyme that exhibits the lowest error rate in the 3´ to 5´ exonucle- ase (proofreading) activity during DNA synthesis in Polymerase Chain Reactions (PCRs). This study was aimed to express and purify Pfu DNA polymerase in a bacterial expression system under a simple purification method. Materials and Methods: Pfu polymerase gene sequence, derived from Pyrocuccus furiosus (Pfu) genomic DNA, was cloned and overexpressed in E. coli BL21 (DE3) pLysS. Upon overexpression, bacterial lysate containing the Pfu DNA polymerase was heated at 94°C for 5 minutes. Pfu DNA polymerase having high thermal stability was retained while the other bacterial proteins were denatured. The resulting thermo stable Pfu DNA polymerase was separated from the other debris of the dena- tured proteins by simple centrifugation. Results: The enzymatic activity of the resulting Pfu DNA polymerase was estimated by comparing with the commer- cial Pfu DNA Polymerases. An estimated 50000 units of functional Pfu DNA polymerase was produced from a 400 ml culture.
    [Show full text]
  • Genomics-Informed Isolation and Characterization of a Symbiotic Nanoarchaeota System from a Terrestrial Geothermal Environment
    Portland State University PDXScholar Biology Faculty Publications and Presentations Biology 7-5-2016 Genomics-Informed Isolation and Characterization of a Symbiotic Nanoarchaeota System from a Terrestrial Geothermal Environment Louie Wurch Oak Ridge National Laboratory Richard J. Giannone Oak Ridge National Laboratory Bernard S. Belisle Oak Ridge National Laboratory Carolyn Swift Oak Ridge National Laboratory Sagar Utturkar Oak Ridge National Laboratory See next page for additional authors Follow this and additional works at: https://pdxscholar.library.pdx.edu/bio_fac Part of the Biology Commons, and the Environmental Sciences Commons Let us know how access to this document benefits ou.y Citation Details Wurch, L. et al. Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment. Nat. Commun. 7:12115 doi: 10.1038/ncomms12115 (2016). This Article is brought to you for free and open access. It has been accepted for inclusion in Biology Faculty Publications and Presentations by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. Authors Louie Wurch, Richard J. Giannone, Bernard S. Belisle, Carolyn Swift, Sagar Utturkar, Robert L. Hettich, Anna-Louise Reysenbach, and Mircea Podar This article is available at PDXScholar: https://pdxscholar.library.pdx.edu/bio_fac/120 ARTICLE Received 11 Mar 2016 | Accepted 1 Jun 2016 | Published 5 Jul 2016 DOI: 10.1038/ncomms12115 OPEN Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment Louie Wurch1,2,w, Richard J. Giannone1, Bernard S. Belisle1,2, Carolyn Swift1,2, Sagar Utturkar1, Robert L. Hettich1,2, Anna-Louise Reysenbach3 & Mircea Podar1,2 Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured.
    [Show full text]
  • Modified Thermostable Dna Polymerase From
    (19) & (11) EP 1 154 017 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12N 9/12 (2006.01) C12Q 1/68 (2006.01) 20.01.2010 Bulletin 2010/03 C12N 15/09 (2006.01) (21) Application number: 01111032.7 (22) Date of filing: 08.05.2001 (54) MODIFIED THERMOSTABLE DNA POLYMERASE FROM PYROCOCCUS KODAKARENSIS MODIFIZIERTE THERMOSTABILE DNA POLYMERASE VON PYROCOCCUS KODAKARAENSIS POLYMERASE D’ADN THERMOASTABLE MODIFIEE DE PYROCOCCUS KODAKARAENSIS (84) Designated Contracting States: • Kawamura, Yoshihisa, CH DE FR GB IT LI SE Tsuruga Inst. of Biotechn. Tsuruga-shi, (30) Priority: 11.05.2000 JP 2000138796 Fukui-ken (JP) • Imanaka, Tadayuki (43) Date of publication of application: Suita-shi, 14.11.2001 Bulletin 2001/46 Osaka-fu (JP) (73) Proprietor: Toyo Boseki Kabushiki Kaisha (74) Representative: Helbing, Jörg et al Osaka-shi, Osaka-fu (JP) Patentanwälte von Kreisler Selting Werner (72) Inventors: Postfach 10 22 41 • Kuroita, Toshihiro, 50462 Köln (DE) Tsuruga Inst. of Biotechnology Tsuruga-shi, (56) References cited: Fukui-ken (JP) EP-A- 0 745 675 EP-A- 0 822 256 • Kitabayashi, Masao, JP-A- 10 042 871 Tsuruga Inst. of Biotechnology Tsuruga-shi, • KONG HUIMIN ET AL: "Characterization of a DNA Fukui-ken (JP) polymerase from the hyperthermophile archaea • Ishida, Yoshikazu, Thermococcus litoralis: Vent DNA polymerase, Tsuruga Inst. of Biotechnology steady state kinetics, thermal stability, Tsuruga-shi, processivity, strand displacement, and Fukui-ken (JP) exonuclease activities." JOURNAL OF • Komatsubara, Hideyuki, BIOLOGICAL CHEMISTRY, vol. 268, no. 3, 1993, Tsuruga Inst. of Biotech. pages 1965-1975, XP000611227 ISSN: 0021-9258 Tsuruga-shi, • UEMORI TAKASHI ET AL: "The Fukui-ken (JP) hyperthermophilic archaeon Pyrodictium • Nishiya, Yoshiaki, occultum has two alpha-like DNA polymerases." Tsuruga Inst.
    [Show full text]