The Telomerase Reverse Transcriptase Subunit from the Dimorphic Fungus Ustilago Maydis
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Introduction of Human Telomerase Reverse Transcriptase to Normal Human Fibroblasts Enhances DNA Repair Capacity
Vol. 10, 2551–2560, April 1, 2004 Clinical Cancer Research 2551 Introduction of Human Telomerase Reverse Transcriptase to Normal Human Fibroblasts Enhances DNA Repair Capacity Ki-Hyuk Shin,1 Mo K. Kang,1 Erica Dicterow,1 INTRODUCTION Ayako Kameta,1 Marcel A. Baluda,1 and Telomerase, which consists of the catalytic protein subunit, No-Hee Park1,2 human telomerase reverse transcriptase (hTERT), the RNA component of telomerase (hTR), and several associated pro- 1School of Dentistry and 2Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California teins, has been primarily associated with maintaining the integ- rity of cellular DNA telomeres in normal cells (1, 2). Telomer- ase activity is correlated with the expression of hTERT, but not ABSTRACT with that of hTR (3, 4). Purpose: From numerous reports on proteins involved The involvement of DNA repair proteins in telomere main- in DNA repair and telomere maintenance that physically tenance has been well documented (5–8). In eukaryotic cells, associate with human telomerase reverse transcriptase nonhomologous end-joining requires a DNA ligase and the (hTERT), we inferred that hTERT/telomerase might play a DNA-activated protein kinase, which is recruited to the DNA role in DNA repair. We investigated this possibility in nor- ends by the DNA-binding protein Ku. Ku binds to hTERT mal human oral fibroblasts (NHOF) with and without ec- without the need for telomeric DNA or hTR (9), binds the topic expression of hTERT/telomerase. telomere repeat-binding proteins TRF1 (10) and TRF2 (11), and Experimental Design: To study the effect of hTERT/ is thought to regulate the access of telomerase to telomere DNA telomerase on DNA repair, we examined the mutation fre- ends (12, 13). -
Mutations That Separate the Functions of the Proofreading Subunit of the Escherichia Coli Replicase
G3: Genes|Genomes|Genetics Early Online, published on April 15, 2015 as doi:10.1534/g3.115.017285 Mutations that separate the functions of the proofreading subunit of the Escherichia coli replicase Zakiya Whatley*,1 and Kenneth N Kreuzer*§ *University Program in Genetics & Genomics, Duke University, Durham, NC 27705 §Department of Biochemistry, Duke University Medical Center, Durham, NC 27710 1 © The Author(s) 2013. Published by the Genetics Society of America. Running title: E. coli dnaQ separation of function mutants Keywords: DNA polymerase, epsilon subunit, linker‐scanning mutagenesis, mutation rate, SOS response Corresponding author: Kenneth N Kreuzer, Department of Biochemistry, Box 3711, Nanaline Duke Building, Research Drive, Duke University Medical Center, Durham, NC 27710 Phone: 919 684 6466 FAX: 919 684 6525 Email: [email protected] 1 Present address: Department of Biology, 300 N Washington Street, McCreary Hall, Campus Box 392, Gettysburg College, Gettysburg, PA 17325 Phone: 717 337 6160 Fax: 7171 337 6157 Email: [email protected] 2 ABSTRACT The dnaQ gene of Escherichia coli encodes the ε subunit of DNA polymerase III, which provides the 3’ 5’ exonuclease proofreading activity of the replicative polymerase. Prior studies have shown that loss of ε leads to high mutation frequency, partially constitutive SOS, and poor growth. In addition, a previous study from our lab identified dnaQ knockout mutants in a screen for mutants specifically defective in the SOS response following quinolone (nalidixic acid) treatment. To explain these results, we propose a model whereby in addition to proofreading, ε plays a distinct role in replisome disassembly and/or processing of stalled replication forks. -
"Protein Quaternary Structure: Subunit&Ndash;Subunit
Protein Quaternary Secondary article Structure: Subunit–Subunit Article Contents . Introduction Interactions . Quaternary Structure Assembly . Folding and Function Susan Jones, University College, London, England . Protein–Protein Recognition Sites . Concluding Remarks Janet M Thornton, University College, London, England The quaternary structure of proteins is the highest level of structural organization observed in these macromolecules. The multimeric proteins that result from quaternary structure formation involve the association of protein subunits through hydrophobic and electrostatic interactions. Protein quaternary structure has important implications for protein folding and function. Introduction from, other components. Using these definitions, the Proteins are organized into a structural hierarchy. The haemoglobin tetramer (comprised of two a and two b polypeptide chain at the primary structural level comprises polypeptide chains) is defined as an oligomer consisting of a linear, noncovalently linked amino acid residue se- two protomers, each consisting of two monomers, i.e. one a quence. Secondary structure is the level at which the linear and one b polypeptide chain. The definition of a subunit sequences aggregate to form structural motifs such as allows the term to be used for either the a-orb-monomer, helices and sheets. The tertiary structure is formed by or for the ab-protomer. The term multimer is also widely packing of the secondary structural elements into one or used in the literature and is defined here as a protein with a more compact globular domains. In many cases proteins finite number of subunits that need not be identical. are composed of only a single polypeptide chain that has The quaternary nature of some proteins was first tertiary structure as its highest level of organization, e.g. -
DNA POLYMERASE III HOLOENZYME: Structure and Function of a Chromosomal Replicating Machine
Annu. Rev. Biochem. 1995.64:171-200 Copyright Ii) 1995 byAnnual Reviews Inc. All rights reserved DNA POLYMERASE III HOLOENZYME: Structure and Function of a Chromosomal Replicating Machine Zvi Kelman and Mike O'Donnell} Microbiology Department and Hearst Research Foundation. Cornell University Medical College. 1300York Avenue. New York. NY }0021 KEY WORDS: DNA replication. multis ubuni t complexes. protein-DNA interaction. DNA-de penden t ATPase . DNA sliding clamps CONTENTS INTRODUCTION........................................................ 172 THE HOLO EN ZYM E PARTICL E. .......................................... 173 THE CORE POLYMERASE ............................................... 175 THE � DNA SLIDING CLAM P............... ... ......... .................. 176 THE yC OMPLEX MATCHMAKER......................................... 179 Role of ATP . .... .............. ...... ......... ..... ............ ... 179 Interaction of y Complex with SSB Protein .................. ............... 181 Meclwnism of the yComplex Clamp Loader ................................ 181 Access provided by Rockefeller University on 08/07/15. For personal use only. THE 't SUBUNIT . .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. 182 Annu. Rev. Biochem. 1995.64:171-200. Downloaded from www.annualreviews.org AS YMMETRIC STRUC TURE OF HOLO EN ZYM E . 182 DNA PO LYM ER AS E III HOLO ENZ YME AS A REPLIC ATING MACHINE ....... 186 Exclwnge of � from yComplex to Core .................................... 186 Cycling of Holoenzyme on the LaggingStrand -
Restoration of Mir-193A Expression Is Tumor-Suppressive in MYC
Bharambe et al. Acta Neuropathologica Communications (2020) 8:70 https://doi.org/10.1186/s40478-020-00942-5 RESEARCH Open Access Restoration of miR-193a expression is tumor-suppressive in MYC amplified Group 3 medulloblastoma Harish Shrikrishna Bharambe1,2, Annada Joshi1, Kedar Yogi1,2, Sadaf Kazi1 and Neelam Vishwanath Shirsat1,2* Abstract Medulloblastoma, a highly malignant pediatric brain tumor, consists of four molecular subgroups, namely WNT, SHH, Group 3, and Group 4. The expression of miR-193a, a WNT subgroup-specific microRNA, was found to be induced by MYC, an oncogenic target of the canonical WNT signaling. MiR-193a is not expressed in Group 3 medulloblastomas, despite MYC expression, as a result of promoter hypermethylation. Restoration of miR-193a expression in the MYC amplified Group 3 medulloblastoma cells resulted in inhibition of growth, tumorigenicity, and an increase in radiation sensitivity. MAX,STMN1, and DCAF7 were identified as novel targets of miR-193a. MiR- 193a mediated downregulation of MAX could suppress MYC activity since it is an obligate hetero-dimerization partner of MYC. MYC induced expression of miR-193a, therefore, seems to act as a feedback inhibitor of MYC signaling. The expression of miR-193a resulted in widespread repression of gene expression that included not only several cell cycle regulators, WNT, NOTCH signaling genes, and those encoding DNA replication machinery, but also several chromatin modifiers like SWI/SNF family genes and histone-encoding genes. MiR-193a expression brought about a reduction in the global levels of H3K4me3, H3K27ac, the histone marks of active chromatin, and an increase in the levels of H3K27me3, a repressive chromatin mark. -
Metabolic Genes.Xlsx
Table S4 Survey of key functional genes with biogeochemical or energetic importance in the genomes of Tardiphaga isolates. The gene list was complied from the FunGen pipeline (http://fungene.cme.msu.edu/) and the authors' own collection. Category Gene Enzyme vice154 vice278 vice304 vice352 C metabolism scd2 esterase / lipase ●●●● C metabolism xylA xylose isomerase ○○○○ One carbon metabolism cooS carbon monoxide dehydrogenase ○○○○ One carbon metabolism pmoA particulate methane monooxygenase A‐subunit ○○○○ One carbon metabolism pxmA1 particulate methane monooxygenase beta subunit ○○○○ One carbon metabolism prk phosphoribulokinase ●●●● One carbon metabolism cbbL ribulose‐bisphosphate carboxylase large subunit ●●●● One carbon metabolism cbbM ribulose‐bisphosphate carboxylase small subunit ●●●● One carbon metabolism smmo soluble methane monooxygenase ●●●● N metabolism amiE aliphatic amidase ●●●● N metabolism amoA ammonia monooxygenase subunit A ○○○○ N metabolism ansA asparaginase ○○○○ N metabolism aspA aspartate ammonia‐lyase ○○○○ N metabolism glsA glutaminase ●●●● N metabolism hutH histidine ammonia‐lyase ○○○○ N metabolism norB nitric oxide reductase ○○○○ N metabolism p450nor nitric oxide reductase (NAD(P), nitrous oxide‐forming) ○○○○ N metabolism nir nitrite reductase ●●●● N metabolism nifH nitrogenase iron protein ○○○○ N metabolism anfD nitrogenase iron‐iron protein, alpha chain ○○○○ N metabolism nifD nitrogenase molybdenum‐iron protein subunit alpha ○○○○ N metabolism vnfD nitrogenase vanadium‐iron protein alpha chain ○○○○ N metabolism nosZ -
Rnase-H-Based Assays Utilizing Modified Rna
(19) TZZ ¥_T (11) EP 2 279 263 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12Q 1/68 (2006.01) 04.09.2013 Bulletin 2013/36 (86) International application number: (21) Application number: 09739895.2 PCT/US2009/042454 (22) Date of filing: 30.04.2009 (87) International publication number: WO 2009/135093 (05.11.2009 Gazette 2009/45) (54) RNASE-H-BASED ASSAYS UTILIZING MODIFIED RNA MONOMERS TESTS AUF RNASE-H-BASIS MIT MODIFIZIERTEN RNA-MONOMEREN DOSAGES À BASE DE RNASE-H UTILISANT DES MONOMÈRES D’ARN MODIFIÉS (84) Designated Contracting States: • ROSE, Scott AT BE BG CH CY CZ DE DK EE ES FI FR GB GR Coralville, IA 52241 (US) HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL • DOBOSY, Joseph PT RO SE SI SK TR Coralville, IA 52241 (US) (30) Priority: 30.04.2008 US 49204 P (74) Representative: Grünecker, Kinkeldey, Stockmair & Schwanhäusser (43) Date of publication of application: Leopoldstrasse 4 02.02.2011 Bulletin 2011/05 80802 München (DE) (60) Divisional application: (56) References cited: 13173388.3 EP-A- 1 367 136 WO-A-01/21813 13173389.1 WO-A-03/074724 WO-A-2004/059012 13173390.9 WO-A-2007/062495 WO-A2-2005/021776 13173391.7 WO-A2-2007/141580 US-A- 5 744 308 US-A- 5 830 664 (73) Proprietor: Integrated Dna Technologies, Inc. Coralville, IA 52241 (US) • ITAYA M ET AL: "Molecular cloning of a ribonuclease H (RNase HI) gene from an extreme (72) Inventors: thermophile Thermus thermophilus HB8: a • WALDER, Joseph, Alan thermostable RNase H can functionally replace Chicago, IL 60645 (US) the Escherichia coli enzyme in vivo." NUCLEIC • BEHLKE, Mark, Aaron ACIDS RESEARCH 25 AUG 1991, vol. -
Every Detail Matters. That Is, How the Interaction Between Gα Proteins and Membrane Affects Their Function
membranes Review Every Detail Matters. That Is, How the Interaction between Gα Proteins and Membrane Affects Their Function Agnieszka Polit * , Paweł Mystek and Ewa Błasiak Department of Physical Biochemistry, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland; [email protected] (P.M.); [email protected] (E.B.) * Correspondence: [email protected]; Tel.: +48-12-6646156 Abstract: In highly organized multicellular organisms such as humans, the functions of an individ- ual cell are dependent on signal transduction through G protein-coupled receptors (GPCRs) and subsequently heterotrimeric G proteins. As most of the elements belonging to the signal transduction system are bound to lipid membranes, researchers are showing increasing interest in studying the accompanying protein–lipid interactions, which have been demonstrated to not only provide the environment but also regulate proper and efficient signal transduction. The mode of interaction between the cell membrane and G proteins is well known. Despite this, the recognition mechanisms at the molecular level and how the individual G protein-membrane attachment signals are interre- lated in the process of the complex control of membrane targeting of G proteins remain unelucidated. This review focuses on the mechanisms by which mammalian Gα subunits of G proteins interact with lipids and the factors responsible for the specificity of membrane association. We summarize recent data on how these signaling proteins are precisely targeted to a specific site in the membrane region by introducing well-defined modifications as well as through the presence of polybasic regions Citation: Polit, A.; Mystek, P.; within these proteins and interactions with other components of the heterocomplex. -
Telomerase Reverse Transcriptase Expression Elevated by Avian Leukosis Virus Integration in B Cell Lymphomas
Telomerase reverse transcriptase expression elevated by avian leukosis virus integration in B cell lymphomas Feng Yang, Rena R. Xian*, Yingying Li, Tatjana S. Polony, and Karen L. Beemon† Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 Communicated by Saul Roseman, The Johns Hopkins University, Baltimore, MD, September 26, 2007 (received for review May 11, 2007) Simple retroviruses induce tumors by integrating into the host integration sites are believed to result from strong biological genome, activating cellular oncogenes and microRNAs, or inacti- selection (7). vating tumor suppressor genes. The identification of these genes Avian leukosis virus (ALV) is a simple retrovirus that does not elucidates molecular mechanisms of tumorigenesis. In this study, encode an oncogene but that can induce tumors by integrating we identified avian leukosis virus (ALV) proviral integration sites in near oncogenes, introducing a strong promoter or enhancer rapid-onset B cell lymphomas arising <12 weeks after infection of sequence (8–12). Typically, ALV induces B cell lymphomas to chicken embryos. By using inverse PCR, 28 unique viral integration develop in Ϸ6 months and frequently involves proviral integra- sites were identified in rapid-onset tumors. Integrations in the tions, resulting in deregulation of the cellular transcription telomerase reverse transcriptase (TERT) promoter/enhancer region factor, myc, as well as bic (precursor to microRNA 155) (10–12). were observed in four different tumors, suggesting that this is a In addition, B cell lymphomas with a more rapid onset (lethal in common integration site. These provirus integrations ranged from Ͻ3 months) have been observed with clonal proviral insertions 217 to 2,584 bp upstream of the TERT transcription initiation site into the myb gene locus, resulting in overexpression of a trun- and were all in the opposite transcriptional orientation to TERT. -
Telomerase Catalysis: a Phylogenetically Conserved Reverse Transcriptase
Proc. Natl. Acad. Sci. USA Vol. 95, pp. 8415–8416, July 1998 Commentary Telomerase catalysis: A phylogenetically conserved reverse transcriptase Victoria Lundblad Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 Replication of telomeres, the ends of eukaryotic chromo- replication and maintenance. As a consequence, the first two somes, is the responsibility of the enzyme telomerase. Since its telomerase-associated proteins, p80 and p95, were identified discovery 13 years ago, research on this unusual DNA poly- after purification of the Tetrahymena telomerase complex (15). merase has revealed a series of surprises. The first of these was On the basis of limited sequence similarities with other poly- the realization that information within the enzyme itself merases, p95 was proposed to contain the catalytic active site determines the sequence of its product: a portion of a telom- of this enzyme (15). However, p95 showed no homology to the erase RNA subunit is the template that dictates the nucleotides emerging family of TERT proteins. This presented a potential added onto the telomere (1, 2). The interest in telomere puzzle, invoking the possibility of an alternative class of replication has increased further during the past several years telomerase enzymes that utilized a different catalytic mecha- because of observations indicating that maintenance of telo- nism. mere length by telomerase could provide the molecular basis This possibility has now been laid to rest by two reports in for determining the lifespan of cells in culture (3). this issue, from the Cech and Collins laboratories, showing that The most recent insight has been the discovery that telom- the Tetrahymena telomerase relies on a reverse transcriptase erase is a reverse transcriptase (4, 5), with catalysis provided subunit for catalysis (7, 13). -
A Screen for Saccharomyces Cerevisiae Essential Genes with an Opi- Phenotype
A Screen for Saccharomyces cerevisiae Essential Genes with an Opi‐ Phenotype Bryan Salas‐Santiago and John M. Lopes 1 Department of Microbiology, and Molecular Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003 1Address for correspondence. University of Massachusetts, 639 North Pleasant St. Amherst, MA 01003. E‐mail: [email protected]. DOI: 10.1534/g3.113.010140 Table S1 List of essential genes with an Opi- phenotype. Gene Aliases Function Subunit of a heterodimeric nuclear SUMO activating enzyme (E1) with Uba2p; activates Smt3p AOS1 RHC31 (SUMO) before its conjugation to proteins (sumoylation) Acetyl-coA synthetase isoform which, along with Acs1p, is the nuclear source of acetyl-coA for ACS2 histone acetylation; mutants affect global transcription ATPase of the CDC48/PAS1/SEC18 (AAA) family, forms a hexameric complex; is essential for AFG2 DRG1 pre-60S maturation and release of several preribosome maturation factors Catalytic component of UDP-GlcNAc transferase, required for the second step of dolichyl-linked ALG13 oligosaccharide synthesis; anchored to the ER membrane via interaction with Alg14p ALG2 Mannosyltransferase that catalyzes two consecutive steps in the N-linked glycosylation pathway Subunit of the ARP2/3 complex, which is required for the motility and integrity of cortical actin ARC40 patches Nuclear actin-related protein involved in chromatin remodeling, component of chromatin- ARP4 ACT3 remodeling enzyme complexes including NuA4 complex CDC11 PSL9 Component of the septin -
Detecting, Identifying, and Disrupting Protein-Protein Interactions
Detecting, Identifying, and Disrupting Protein-Protein Interactions by Sang-Hyun Park A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Biochemistry) at the UNIVERSITY OF WISCONSIN - MADISON 1999 A dissertation entitled Detecting, Identifying, and Disrupting Protein-Protein Interactions .... ~,. submitted to the Graduate School of the University of Wisconsin-Madison ~ in partial fulfillment of the requirements for the ~J degree of Doctor of Philosophy by Sang-Hyun Park Date of Final Oral Examination: December l3, 1999 Month & Year Degree to be awarded: December 1 9 9 9 May August l-s: **.****************************~********************** ~.Qf.J~_"ion Readers: Signature, Dean of Graduate School -~ '(1fvti6.5- ~(M~/ifH i ACKNOWLEDGMENTS I am grateful to James Hu, Jordan Tang and Martin Chalfie for providing bacterial strains and plasmids. I also thank Chiwook Park for providing the wild-type RNase A used in Chapter 3. Ronald Raines has been a superior advisor. I thank Ron for his support for my study. He allowed for the freedom of creativity and the freedom of work hour. Genetic selection and screens developed in this thesis owes a lot to frustrations with the yeast two-hybrid screening on which I spent the first two years of my graduate study. This thesis was partially supported by a Korean Government Fellowship for Overseas Study. I must thank my family for their patience and support for my studying abroad. [ cannot thank enough my wife, Nam-Sook Baik, who has endured a great deal of agony and joy together with me throughout the days in Madison. [ want to say sorry to my son, Albert (~ ~), for my occasional absence from him when he needed me.