In Vitro and in Vivo Models Analyzing Von Hippel-Lindau Disease-Specific Mutations

Total Page:16

File Type:pdf, Size:1020Kb

In Vitro and in Vivo Models Analyzing Von Hippel-Lindau Disease-Specific Mutations [CANCER RESEARCH 64, 8595–8603, December 1, 2004] In vitro and In vivo Models Analyzing von Hippel-Lindau Disease-Specific Mutations W. Kimryn Rathmell,1,3 Michele M. Hickey,1,2 Natalie A. Bezman,1 Christie A. Chmielecki,3 Natalie C. Carraway,3 and M. Celeste Simon1,2 1Abramson Family Cancer Research Institute and the Department of Cell and Molecular Biology, and 2Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, Pennsylvania; and 3Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina ABSTRACT transport and droplet formation (8, 9). Unregulated expression of the full complement of hypoxia response genes is surmised to contribute Mutations in the von Hippel-Lindau (VHL) tumor suppressor gene much of the clinical and pathological phenotype of renal cell carci- cause tissue-specific tumors, with a striking genotype-phenotype correla- noma, which is characterized as a highly vascular, glycolytic, lipid- tion. Loss of VHL expression predisposes to hemangioblastoma and clear cell renal cell carcinoma, whereas specific point mutations predispose to rich tumor that can be associated with polycythemia (10, 11). Detailed pheochromocytoma, polycythemia, or combinations of hemangioblas- studies of the effects of VHL loss have identified the regulation of the toma, renal cell carcinoma, and/or pheochromocytoma. The VHL protein hypoxia response pathway via the proteasomal degradation of HIF1␣ (pVHL) has been implicated in many cellular activities including the and HIF2␣ as a major activity of the VHL protein (pVHL; refs. hypoxia response, cell cycle arrest, apoptosis, and extracellular matrix 12–15). The pVHL acts as the substrate receptor for an E3 ubiquitin Ϫ Ϫ remodeling. We have expressed missense pVHL mutations in Vhl / ligase complex and targets HIF1␣ and HIF2␣ for degradation under murine embryonic stem cells to test genotype-phenotype correlations in normal oxygen (O2) tension (16). The O2-dependent regulation of euploid cells. We first examined the ability of mutant pVHL to direct HIF␣ (referring to either HIF1␣ or HIF2␣) is imparted by posttrans- degradation of the hypoxia inducible factor (HIF) subunits HIF1␣ and lational hydroxylation of specific prolines located in the HIF␣ O - HIF2␣. All mutant pVHL proteins restored proper hypoxic regulation of 2 ␣ HIF1␣, although one VHL mutation (VHLR167Q) displayed impaired bind- dependent degradation domain by HIF prolyl hydroxylases (17–19). ␣ ␣ ing to Elongin C. This mutation also failed to restore HIF2␣ regulation. In When O2 levels drop, HIF1 and HIF2 accumulate (5). In the separate assays, these embryonic stem cells were used to generate terato- absence of pVHL, HIF1␣ and HIF2␣ are maximally stabilized in mas in immunocompromised mice, allowing independent assessment of the presence of atmospheric O2 levels and show no additional O2- the effects of specific VHL mutations on tumor growth. Surprisingly, dependent accumulation (13). Y112H teratomas expressing the VHL mutant protein displayed a growth We previously reported that VhlϪ/Ϫ murine embryonic stem cells ␣ Ϫ Ϫ disadvantage, despite restoring HIF regulation. Finally, we observed predictably disrupt the hypoxia response pathway (20). In Vhl / increased microvessel density in teratomas derived from VhlϪ/Ϫ as well as embryonic stem cells, HIF1␣ and HIF2␣ are highly expressed under VHLY112H, VHLR167Q, and VHLR200W embryonic stem cells. Together, these observations support the hypothesis that pVHL plays multiple roles in the normoxic conditions, and protein levels are not additionally stabilized cell, and that these activities can be separated via discrete VHL point in response to O2 deprivation. Furthermore, Vhl deletion gives rise to mutations. The ability to dissect specific VHL functions with missense highly glycolytic cells, as would be expected in cells with elevated Ϫ Ϫ mutations in a euploid model offers a novel opportunity to elucidate the levels of glycolytic enzymes. When Vhl / embryonic stem cells are activities of VHL as a tumor suppressor. grown in a teratoma model system the tumors display a highly vascular phenotype, although with a surprising reduction in tumor volume (20). INTRODUCTION The spectrum of tumors arising in individual VHL patients strongly Mutations in the von Hippel-Lindau (VHL) tumor suppressor gene correlates with specific VHL mutations (21, 22), and the syndrome has give rise to a variety of tumors and other abnormalities in affected been divided into type 1 and type 2 disease based on predisposition for individuals including renal clear cell carcinoma, pheochromocytoma, pheochromocytoma (Fig. 1A). Type 1 disease is characterized by hemangioblastoma, and polycythemia (1). Some of these disease mutations, which delete, silence, or destabilize the VHL gene, and this manifestations derive from the unregulated expression of the hypoxia patient group has a low frequency of pheochromocytoma (23). Type inducible factor (HIF) transcription complex. HIF is a heterodimer 2 disease is characterized by a strong predisposition for pheochromo- composed of a highly regulated ␣ subunit (either HIF1␣ or HIF2␣/ cytoma, and it is additionally subdivided into 2A (pheochromocy- EPAS1) and a ubiquitously expressed ␤ subunit (HIF1␤/ARNT; refs. toma, hemangioblastoma, and low risk for renal cell carcinoma), 2B 2–4). This complex, in cooperation with the coactivators cAMP- (pheochromocytoma, hemangioblastoma, and high risk for renal cell responsive element binding protein and p300, activates transcription carcinoma), and 2C (pheochromocytoma only). Molecular analysis of via a hypoxia response element in the promoter or enhancer regions of these mutations shows that type 2A mutants and type 2C mutants many hypoxia-responsive genes. Genes transcriptionally activated by maintain interaction with the ubiquitin ligase complex, whereas 2B HIF include factors involved in angiogenesis, glucose transport, gly- mutants are deficient in this interaction (23). In addition, homozygos- colysis, and erythropoiesis as recently reviewed (5–7), and lipid ity for a VHL mutation in the extreme COOH-terminal domain has been associated with a highly penetrant congenital form of polycy- Received 4/22/04; revised 9/8/04; accepted 10/1/04. themia termed Chuvash Polycythemia (24, 25). No tumor predispo- Grant support: NIH Grant K08-CA098410 and a V Foundation Scholar Award sition has yet been identified with this mutation. (W. Rathmell), Howard Hughes Medical Institute Predoctoral Fellowships and the Ruth L. Kirschstein National Research Service Award (M. Hickey and N. Bezman), and NIH In addition to VHL disease, mutations in VHL have been identified Grant HL66130 and the Howard Hughes Medical Institute (M. Simon). in the majority of patients with sporadic clear cell renal cell carcinoma The costs of publication of this article were defrayed in part by the payment of page (26–28), which constitutes the majority of carcinomas of the kidney. charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. This form of renal cell carcinoma is characterized by a highly vascular Requests for reprints: M. Celeste Simon, University of Pennsylvania, Abramson cystic or solid mass comprised of nests of tumor cells containing Family Cancer Research Institute, BRB II/III, Room 450, Philadelphia, PA 19104. Phone: (215) 746-5526; Fax: (215) 746-5511; E-mail: [email protected]. abundant clear cytoplasm consisting of glycogen and neutral lipid. ©2004 American Association for Cancer Research. Although loss of VHL is not a transforming event in such cells, VHL 8595 Downloaded from cancerres.aacrjournals.org on September 26, 2021. © 2004 American Association for Cancer Research. ANALYSIS OF VHL MUTATIONS Fig. 1. Embryonic stem cell expression of representative VHL missense mutations. A. VHL disease subtypes, characteristic patterns of disease, and mutations used in this analysis to represent each subtype of VHL disease. B, schematic of VHL gene. The hemagglutinin tag is located at the NH2 terminus as indicated. Important residues are identified, as are the known interaction domains. C, human pVHL immunoblot. Protein extracts from embryonic stem cells expressing the indicated version of pVHL, pVHL null, and endogenous mouse pVHL were compared with in vitro translated human pVHL protein. Note the lack of signal in the endogenous pVHL extract from Vhlϩ/Ϫ extracts. D, murine pVHL immunoblot. Protein extracts from pVHL wild-type, heterozygous, and null embryonic stem cells. (HA, hemagglutinin) mutations have been identified in renal cysts and dysplastic lesions, ally, the mutation associated with VHL type 2B disease (VHLR167Q) strongly suggesting they represent an early event in renal tumorigen- uniquely conferred impaired interaction with Elongin C as well as a ␣ ␣ esis (29). Furthermore, renal cell carcinoma cells regain O2-regulated disruption of HIF2 hypoxia responsive regulation, whereas HIF1 gene expression (15, 30) and lose their transformed phenotype on protein regulation remained intact. Additionally, a mutant associated reintroduction of wild-type pVHL activities (31, 32). with VHL type 2A disease (VHLY112H) showed a suppressive growth Whereas VHL clearly regulates the hypoxia response pathway, the effect similar to that observed with Vhl loss in teratomas. Consistent cohort of mutations giving rise to type 2C disease has not been found with previous observations, we detected no impact on the hypoxia to affect
Recommended publications
  • Imperial Life Sciences
    PRICE LIST 2020/21 Genomics Reagents & Consumables Cell & Imaging Advanced Molecular Diagnostics Imperial Life Sciences One Company Complete Solutions + 91 124 4559 800 - 99 [email protected] Imperial life Sciences (P) Ltd Price list 2020-21 (consumables) M/S NEW ENGLAND BIOLABS INC U Price Rs. (2020- Part No Description - without units Unit Size 21) E6442L NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) Set 2 384 rxns 2,47,940.00 E6442S NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) Set 2 96 rxns 68,908.00 E7850L NEBNext rRNA Depletion Kit (Bacteria) 24 rxns 1,39,104.00 E7850S NEBNext rRNA Depletion Kit (Bacteria) 6 rxns 38,254.00 E7850X NEBNext rRNA Depletion Kit (Bacteria) 96 rxns 5,00,388.00 E7860L NEBNext rRNA Depletion Kit (Bacteria) with RNA Sample Purification Beads 24 rxns 1,44,900.00 E7860S NEBNext rRNA Depletion Kit (Bacteria) with RNA Sample Purification Beads 6 rxns 39,284.00 E7860X NEBNext rRNA Depletion Kit (Bacteria) with RNA Sample Purification Beads 96 rxns 5,21,640.00 M0460T T7 RNA Polymerase (High Concentration) 50,000 units 72,643.00 M0467S Salt-T4 DNA Ligase 20,000 units 8,243.00 M0467L Salt-T4 DNA Ligase 100,000 units 32,973.00 M0470T Hi-T7 RNA Polymerase (High Concentration) 50,000 units 87,584.00 M2622L Hi-T4 DNA Ligase 100,000 units 32,973.00 M2622S Hi-T4 DNA Ligase 20,000 units 8,243.00 R0739L BsmBI-v2 1,000 units 38,254.00 R0739S BsmBI-v2 200 units 9,402.00 B0201S T4 Polynucleotide Kinase Reaction Buffer 4.0 ml 3,091.00 B0202S T4 DNA Ligase Reaction Buffer
    [Show full text]
  • 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.
    [Show full text]
  • Artificial Human Telomeres from DNA Nanocircle Templates
    Artificial human telomeres from DNA nanocircle templates Ulf M. Lindstro¨ m*, Ravi A. Chandrasekaran*, Lucian Orbai*, Sandra A. Helquist*, Gregory P. Miller*, Emin Oroudjev†, Helen G. Hansma†, and Eric T. Kool*‡ *Department of Chemistry, Stanford University, Stanford, CA 94305-5080; and †Department of Physics, University of California, Santa Barbara, CA 93106 Edited by Peter B. Dervan, California Institute of Technology, Pasadena, CA, and approved October 9, 2002 (received for review July 3, 2002) Human telomerase is a reverse-transcriptase enzyme that synthe- sizes the multikilobase repeating hexamer telomere sequence (TTAGGG)n at the ends of chromosomes. Here we describe a designed approach to mimicry of telomerase, in which synthetic DNA nanocircles act as essentially infinite catalytic templates for efficient synthesis of long telomeres by DNA polymerase enzymes. Results show that the combination of a nanocircle and a DNA polymerase gives a positive telomere-repeat amplification proto- col assay result for telomerase activity, and similar to the natural enzyme, it is inhibited by a known telomerase inhibitor. We show that artificial telomeres can be engineered on human chromo- somes by this approach. This strategy allows for the preparation of synthetic telomeres for biological and structural study of telomeres and proteins that interact with them, and it raises the possibility of telomere engineering in cells without expression of telomerase itself. Finally, the results provide direct physical support for a recently proposed rolling-circle mechanism for telomerase- independent telomere elongation. rolling-circle replication ͉ primer extension ͉ telomerase ͉ TRAP assay he telomerase enzyme synthesizes the multikilobase repeat- Ting hexamer telomere sequence (TTAGGG)n at the ends of chromosomes (1–3).
    [Show full text]
  • DNA Polymerases Drive DNA Sequencing-By-Synthesis Technologies: Both Past and Present
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE REVIEW ARTICLEprovided by Frontiers - Publisher Connector published: 24 June 2014 doi: 10.3389/fmicb.2014.00305 DNA polymerases drive DNA sequencing-by-synthesis technologies: both past and present Cheng-Yao Chen* Protein Engineering Group, Illumina, San Diego, CA, USA Edited by: Next-generation sequencing (NGS) technologies have revolutionized modern biological and Andrew F.Gardner, New England biomedical research. The engines responsible for this innovation are DNA polymerases; Biolabs, USA they catalyze the biochemical reaction for deriving template sequence information. In fact, Reviewed by: DNA polymerase has been a cornerstone of DNA sequencing from the very beginning. Suleyman Yildirim, Walter Reed Army Institute of Research, USA Escherichia coli DNA polymerase I proteolytic (Klenow) fragment was originally utilized Andreas Marx, University of in Sanger’s dideoxy chain-terminating DNA sequencing chemistry. From these humble Konstanz, Germany beginnings followed an explosion of organism-specific, genome sequence information *Correspondence: accessible via public database. Family A/B DNA polymerases from mesophilic/thermophilic Cheng-Yao Chen, Protein Engineering bacteria/archaea were modified and tested in today’s standard capillary electrophoresis Group, Illumina, 5200 Illumina Way, San Diego, CA 92122, USA (CE) and NGS sequencing platforms.These enzymes were selected for their efficient incor- e-mail: [email protected] poration of bulky dye-terminator and reversible dye-terminator nucleotides respectively. Third generation, real-time single molecule sequencing platform requires slightly different enzyme properties. Enterobacterial phage φ29 DNA polymerase copies long stretches of DNA and possesses a unique capability to efficiently incorporate terminal phosphate- labeled nucleoside polyphosphates.
    [Show full text]
  • Trapping DNA Polymerases Using Triplex-Forming Oligodeoxyribonucleotides*
    Gene, 149 (1994) 1277136 0 1994 Elsevier Science B.V. All rights reserved. 0378-l 119/94/$07.00 127 GENE 08089 Trapping DNA polymerases using triplex-forming oligodeoxyribonucleotides* (DNA polymerization;termination; triplex) George M. Samadashwily and Sergei M. Mirkin Department of Genetics, Unioersitr of I/his at Chicago, Chicago, IL 60612, USA Received by J.W. Larrick: 22 March 1994; Accepted: 25 March 1994; Received at publishers: 16 May 1994 SUMMARY Triplexes (triple helices) formed within DNA templates prior to or during DNA synthesis cause DNA polymerase to terminate [Samadashwily et al., EMBO J. 13 (1993) 4975549831. Here, we show that triplex-forming oligodeoxyribo- nucleotides (oligos) efficiently trap DNA polymerases at target DNA sequences within single-stranded (ss) templates. This was observed for all studied DNA polymerases, including Sequenase and the thermophilic Taq and Vent polymer- ases. The termination rate depends on the fine structure of a triplex, as well as on ambient conditions such as temperature and the concentration of magnesium ions. Inhibition of DNA synthesis was observed not only when triplexes blocked the path of DNA polymerase, but also when a polymerization primer was involved in triplex formation. Escherichia coli ss-binding (SSB) protein helps DNA polymerase overcome the triplex barrier, but with an efficiency dramatically dependent on the triplex configuration. These results describe a novel method for blocking DNA replication at target homopurine-homopyrimidine sequences by means of triplex-forming oligos in direct analogy with similar results during transcription. INTRODUCTION images of chemically similar strands in target DNAs (Mirkin et al., 1987; Beal and Dervan, 1991).
    [Show full text]
  • Investigation of the DNA-Dependent Cyclohexenyl Nucleic Acid
    3828–3836 Nucleic Acids Research, 2005, Vol. 33, No. 12 doi:10.1093/nar/gki695 Investigation of the DNA-dependent cyclohexenyl nucleic acid polymerization and the cyclohexenyl nucleic acid-dependent DNA polymerization Veerle Kempeneers, Marleen Renders, Matheus Froeyen and Piet Herdewijn* Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven, Belgium Received April 11, 2005; Revised May 27, 2005; Accepted June 17, 2005 ABSTRACT conformations when incorporated in different double- stranded DNA sequences, which proves the flexibility of DNA polymerases from different evolutionary families the cyclohexene ring system (5). Since cyclohexenyl nucle- [Vent (exoÀ) DNA polymerase from the B-family poly- osides lack the 20-OH they can be considered as a DNA mimic. 3 merases, Taq DNA polymerase from the A-family Based on their preference for the H2 conformation they might polymerases and HIV reverse transcriptase from the be considered as an RNA mimic. Hybridization of CeNA with reverse transcriptase family] were examined for their both DNA and RNA has been observed (1,6) and introducing ability to incorporate the sugar-modified cyclohexenyl cyclohexenyl nucleotides into the DNA strand of a DNA/RNA nucleoside triphosphates. All enzymes were able to hybrid increases the thermal stability of the duplex. CeNA is use the cyclohexenyl nucleotides as a substrate. also stable against degradation in serum (1). These observa- Using Vent (exoÀ) DNA polymerase and HIV reverse tions were the basis for the investigation of CeNA in siRNA transcriptase, we were even able to incorporate seven experiments and encouraged us to synthesize the triphosphates of cyclohexenyl nucleosides and test them as a substrate for consecutive cyclohexenyl nucleotides.
    [Show full text]
  • Taq DNA Polymerase
    Polymerase Chain Reaction (PCR) • PCR is a technique which is used to amplify the number of copies of a specific region of DNA, in order to produce enough DNA to be adequately tested. • As a result, it now becomes possible to analyze and characterize DNA fragments found in minute quantities in different samples. Polymerase Chain Reaction (PCR) • PCR carry out for – DNA cloning – sequencing, – DNA-based phylogeny, or – functional analysis of genes; – the diagnosis of diseases; – genetic fingerprints and – the detection and diagnosis of infectious diseases. PROCEDURE ….. PCR Reagents • Template DNA (e.g., plasmid DNA, genomic DNA). • Forward and reverse PCR primers. • MgCl2 (25 mM). • dNTPs (a mixture of 2.5 mM dATP, dCTP, dGTP, and dTTP). • PCR buffer: 500 mM KCl, 100 mM Tris-HCl, pH 8.3, 25°C. PCR Reagents • Thermal stable DNA polymerase – DNA polymerases without 3′ → 5′ proofreading activity • Taq DNA polymerase • Tth DNA polymerase • Tfl DNA polymerase – DNA polymerases with 3′ → 5′ proofreading activity: • Pwo DNA polymerase • Pfu DNA polymerase • Tli DNA polymerase • Vent DNA polymerase PCR Reagents • Optional: PCR additives /cosolvents (optional; e.g., • betaine, glycerol, DMSO, formamide, bovine serum albumin, ammonium sulfate, polyethylene glycol, gelatin, Tween-20, Triton X-100, β-mercaptoethanol, or tetramethylammonium chloride). Polymerase Chain Reaction (PCR) • Initialization step: 94–96 °C (or 98 °C if extremely thermostable polymerases are used), for 1–9 minutes. – the complete separation of the DNA strands and unfolding secondary structures – This stage also required for DNA polymerases that require heat activation by hot-start PCR. Polymerase Chain Reaction (PCR) • Denaturation step: 94–98 °C for 20–30 seconds.
    [Show full text]
  • Diacetylchitobiase Gene from Vibrio Parahaemolyticus: Sequence Analysis, Protein Secretion, and Secretion System Development
    Louisiana State University LSU Digital Commons LSU Historical Dissertations and Theses Graduate School 1996 The yC toplasmic N,n'-Diacetylchitobiase Gene From Vibrio Parahaemolyticus: Sequence Analysis, Protein Secretion, and Secretion System Development. Michael Hongli Wu Louisiana State University and Agricultural & Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_disstheses Recommended Citation Wu, Michael Hongli, "The yC toplasmic N,n'-Diacetylchitobiase Gene From Vibrio Parahaemolyticus: Sequence Analysis, Protein Secretion, and Secretion System Development." (1996). LSU Historical Dissertations and Theses. 6171. https://digitalcommons.lsu.edu/gradschool_disstheses/6171 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Historical Dissertations and Theses by an authorized administrator of LSU Digital Commons. For more information, please contact [email protected]. INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps.
    [Show full text]
  • Structural Studies of Terpenoid Biosynthesis And
    STRUCTURAL STUDIES OF TERPENOID BIOSYNTHESIS AND BACTERIAL CELL DIVISION A Dissertation by DONG YANG Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY August 2006 Major Subject: Biochemistry STRUCTURAL STUDIES OF TERPENOID BIOSYNTHESIS AND BACTERIAL CELL DIVISION A Dissertation by DONG YANG Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, James C. Sacchettini Committee Members, James C. Hu Patricia J. Liwang Terry L. Thomas Head of Department, Gregory D. Reinhart August 2006 Major Subject: Biochemistry iii ABSTRACT Structural Studies of Terpenoid Biosynthesis and Bacterial Cell Division. (August 2006) Dong Yang, B.S., Zhe Jiang University Chair of Advisory Committee: Dr. James C. Sacchettini The objective of this work is to investigate the structures of two nucleotide binding proteins: mevalonate kinase (MVK) and FtsZ. MVK is the key enzyme involved in terpenoid biosynthesis. In this study, we solved the crystal structures of the M. jannaschii MVK apoprotein, as well as the protein in complex with ligands. Its fold was analyzed and firmly established within the GHMP kinase family, in which homoserine kinase (HSK), phosphomevalonate kinase and galactokinase also belong. Structural analysis in combination with enzyme kinetics studies revealed the mechanism of this enzyme upon substrate binding, catalysis and inhibition. In particular, the phosphate-binding loop was found to be critically involved in the binding of nucleotides and terpenoids, via the interaction with a di-phosphate moiety from the ligand.
    [Show full text]
  • Allosteric Regulation of Mammalian and Bacterial Fructose-1,6-Bisphosphatases Justin Keith Hines Iowa State University
    Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2007 Allosteric regulation of mammalian and bacterial fructose-1,6-bisphosphatases Justin Keith Hines Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Biochemistry Commons Recommended Citation Hines, Justin Keith, "Allosteric regulation of mammalian and bacterial fructose-1,6-bisphosphatases" (2007). Retrospective Theses and Dissertations. 15778. https://lib.dr.iastate.edu/rtd/15778 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Allosteric regulation of mammalian and bacterial fructose-1,6-bisphosphatases by Justin Keith Hines A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Biochemistry Program of Study Committee: Richard Honzatko, Major Professor Herbert Fromm Alan DiSpirito Reuben Peters Robert Angelici Iowa State University Ames, Iowa 2007 Copyright © Justin Keith Hines, 2007. All rights reserved. 2008 ii TABLE OF CONTENTS LIST OF ABBREVIATIONS v ABSTRACT vii CHAPTER I. GENERAL INTRODUCTION 1 Literature Review 1 Thesis Organization 8 References 10 CHAPTER II: NOVEL
    [Show full text]
  • Accurate and Efficient One-Pot Reverse Transcription and Amplification of 2’ Fluoro-Modified Nucleic Acids by Commercial DNA Polymerases
    Accurate and efficient one-pot reverse transcription and amplification of 2’ fluoro-modified nucleic acids by commercial DNA polymerases Arianna S. Thompson, Susanna E. Barrett, Aurora G. Weiden, Ananya Venkatesh, Madison K. C. Seto, Simone Z. P. Gottlieb and Aaron M. Leconte* W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States of America Corresponding Author *Telephone: 909-607-9353. Email: [email protected] Author Contributions The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript. Funding This work was supported by the National Science Foundation (CHE-1752924 CAREER award to A.M.L.). Notes The authors declare no competing financial interests. ABSTRACT: DNA is a foundational tool in biotechnology and synthetic biology but is limited by sensitivity to DNA-modifying enzymes. Recently, researchers have identified DNA polymerases that can enzymatically synthesize long oligonucleotides of modified-DNA (M-DNA) that are resistant to DNA-modifying enzymes. Most applications require M-DNA to be reverse transcribed, typically using a RNA reverse transcriptase, back into natural DNA for sequence analysis or further manipulation. Here, we tested commercially available DNA-dependent DNA polymerases for their ability to reverse transcribe and amplify M-DNA in a one-pot reaction. Three of the six polymerases chosen (Phusion, Q5, and Deep Vent) were able to reverse transcribe and amplify synthetic 2’F M-DNA in a single reaction with < 5 10-3 errors per base pair. We further used Q5 DNA polymerase to reverse transcribe and amplify M-DNA synthesized by two candidate M-DNA polymerases (SFP1 and SF4-6), allowing for quantification of the frequency, types, and locations of errors made during M-DNA synthesis.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 8,034,568 B2 Kurn Et Al
    US008O34568B2 (12) United States Patent (10) Patent No.: US 8,034,568 B2 Kurn et al. (45) Date of Patent: Oct. 11, 2011 (54) ISOTHERMAL NUCLEICACID 5,427,930 A 6/1995 Birkenmeyer et al. AMPLIFICATION METHODS AND 5.437,990 A 8/1995 Burg et al. 5,455,166 A 10, 1995 Walker COMPOSITIONS 5,480,784. A 1/1996 Kacian et al. 5,491,063 A 2f1996 Fisher et al. (75) Inventors: Nurith Kurn, Palo Alto, CA (US); 5,508,178 A 4/1996 Rose et al. Shenglong Wang, San Ramon, CA (US) 5,510,270 A 4/1996 Fodor et al. 5,545,522 A 8, 1996 Van Gelder et al. 5,554,516 A 9, 1996 Kacian et al. (73) Assignee: NuGEN Technologies, Inc., San Carlos, 5,554,517 A 9/1996 Davey et al. CA (US) 5,556,752 A 9, 1996 Lockhart et al. 5,556,771 A 9, 1996 Shen et al. (*) Notice: Subject to any disclaimer, the term of this 5,565,322 A 10, 1996 Heller patent is extended or adjusted under 35 5,578,832 A 11/1996 Trulson et al. 5,589,339 A 12/1996 Hampson et al. U.S.C. 154(b) by 0 days. 5,595,891 A 1/1997 Rose et al. 5,616,478 A 4/1997 Chetverin et al. (21) Appl. No.: 12/370,534 5,627,275 A 5, 1997 Ro11 5,641,658 A 6/1997 Adams et al. (22) Filed: Feb. 12, 2009 5,648,211 A 7/1997 Fraiser et al.
    [Show full text]