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Transcriptional Units
Proc. Natl. Acad. Sci. USA Vol. 76, No. 7, pp. 3194-3197, July 1979 Biochemistry Cyclic AMP as a modulator of polarity in polycistronic transcriptional units (positive regulation/rho factor/lactose and galactose operons/catabolite repression) AGNES ULLMANNt, EVELYNE JOSEPHt, AND ANTOINE DANCHINt tUnite de Biochimie Cellulaire, Institut Pasteur, 75724 Paris Cedex 15, France; and tInstitut de Biologie Physico-Chimique, 75005 Paris, France Communicated by Frangois Jacob, April 16, 1979 ABSTRACT The degree of natural polarity in the lactose scribed by Watekam et al. (7, 8) in sonicated bacterial extracts. and galactose operons of Escherichia coli is affected by aden- One unit is the amount of enzyme that converts 1 nmol of osine 3',5'-cyclic monophosphate (cAMP). This effect, mediated substrate per min at 280C (except for UDPGal epimerase, for by the cAMP receptor protein, is exerted at sites distinct from the promoter. Experiments performed with a mutant bearing which the assay temperature was 220C). a thermosensitive rho factor activity indicate that cAMP relieves Reagents and Enzymes. They were obtained from the fol- polarity by interfering with transcription termination. Con- lowing companies: trimethoprim from Calbiochem; all radio- flicting results in the literature concerning the role of cAMP active products from Amersham; isopropyl-f3-D-thiogalactoside receptor protein and cAMP in galactose operon expression can (IPTG), D-fucose, cAMP, UDPglucose dehydrogenase, and all be reconciled by the finding that cAMP stimulates the expres- substrates from Sigma; and all other chemicals from Merck. sion of operator distal genes without significantly affecting the proximal genes. Therefore, it appears necessary to reevaluate the classification o(the galactose operon as exhibiting cAMP- RESULTS mediated catabolite repression at the level of transcription Natural Polarity in Lactose Operon. -
Sudips Revised Thesis
Investigation Of The Behavior Of The Gal4 Inhibitor Gal80 Of The GAL Genetic Switch In The Yeast Saccharomyces Cerevisiae Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Sudip Goswami, M.S. Graduate Program in Molecular Genetics The Ohio State University 2014 Dissertation Committee Dr. James Hopper, Advisor Dr. Stephen Osmani Dr. Hay-Oak Park Dr. Jian-Qiu Wu ii Copyright by Sudip Goswami 2014 iii ABSTRACT The DNA-binding transcriptional activator Gal4 and its regulators Gal80 and Gal3 constitute a galactose-responsive switch for the GAL genes of Saccharomyces cerevisiae. Gal4 binds to upstream activation sequences or UASGAL sites on GAL gene promoters as a dimer both in the absence and presence of galactose. In the absence of galactose, a Gal80 dimer binds to and masKs the Gal4 activation domain, inhibiting its activity. In the presence of galactose, Gal3 interacts with Gal80 and relieves Gal80’s inhibition of Gal4 activity allowing rapid induction of expression of GAL genes. In the first part of this work (Chapter 2) in-vitro chemical crosslinking coupled with SDS PAGE and native PAGE analysis were employed to show that the presence of Gal3 that can interact with Gal80 impairs Gal80 self association. In addition, live cell spinning disK confocal imaging showed that dissipation of newly discovered Gal80-2mYFP/2GFP clusters in galactose is dependent on Gal3’s ability to interact with Gal80. In the second part (Chapter 3), extensive analysis of Gal80 clusters was carried out which showed that these clusters associate strongly with the GAL1-10-7 locus and this association is dependent on the presence of the UASGAL sites at this locus. -
NADP, Corepressor for the Bacillus Catabolite Control Protein Ccpa
Proc. Natl. Acad. Sci. USA Vol. 95, pp. 9590–9595, August 1998 Microbiology NADP, corepressor for the Bacillus catabolite control protein CcpA JEONG-HO KIM,MARTIN I. VOSKUIL, AND GLENN H. CHAMBLISS* Department of Bacteriology, University of Wisconsin-Madison, E. B. Fred Hall, Madison, WI 53706 Communicated by T. Kent Kirk, University of Wisconsin, Madison, WI, June 10, 1998 (received for review February 12, 1998) ABSTRACT Expression of the a-amylase gene (amyE)of (18), and the presence of a conserved effector-binding domain Bacillus subtilis is subject to CcpA (catabolite control protein in CcpA (3) together strongly suggest the necessity of an A)-mediated catabolite repression, a global regulatory mech- effector(s) such as a corepressor to activate CcpA. To date, anism in Bacillus and other Gram-positive bacteria. To deter- HPr, a phosphocarrier protein in the phosphoenolpyruvate- mine effectors of CcpA, we tested the ability of glycolytic :sugar phosphotransferase system, and two glycolytic metab- metabolites, nucleotides, and cofactors to affect CcpA binding olites, fructose-1,6-diphosphate (FDP) and glucose-6- to the amyE operator, amyO. Those that stimulated the phosphate, have been proposed as effectors of CcpA (19–22). DNA-binding affinity of CcpA were tested for their effect on HPr is phosphorylated in two different fashions: ATP- transcription. HPr-P (Ser-46), proposed as an effector of dependent phosphorylation at Ser-46 and phosphoenolpyru- CcpA, also was tested. In DNase I footprint assays, the affinity vate-dependent phosphorylation at His-15 (23). In the ptsH1 of CcpA for amyO was stimulated 2-fold by fructose-1,6- mutant strain, the serine residue at position 46 of HPr is diphosphate (FDP), 1.5-fold by oxidized or reduced forms of replaced with an alanine, which eliminates phosphorylation of NADP, and 10-fold by HPr-P (Ser-46). -
Studies with the Escherichia Coli Galactose Operon Regulatory Region Carrying a Point Mutation That Simultaneously Inactivates T
CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector Volume 219, number 1, 189-196 FEB 04899 July 1987 Studies with the Escherichia coli galactose operon regulatory region carrying a point mutation that simultaneously inactivates the two overlapping promoters Interactions with RNA polymerase and the cyclic AMP receptor protein Sreenivasan Ponnambalarn, Annick Spassky* and Stephen Busby Department of Biochemistry, University of Birmingham, PO Box 363, Birmingham B15 2TT, England and *D~partement de Biologie Molbculaire, lnstitut Pasteur, 25 Rue du Dr Roux, 75724 Paris Cedex 15, France Received 22 April 1987 We report in vitro studies of the interactions between purified E. coli RNA polymerase and DNA from the regulatory region of the E. coli galactose operon which carries a point mutation that simultaneously stops transcription initiation at the two normal start points, $1 and $2. In the presence of this point muta- tion, transcription initiates at a third start point 14/15 bp downstream of $1, showing that inactivation of the two normally active promoters, P1 and P2, unmasks a third weaker promoter, P3. Transcription initia- tion in the gal operon is normally regulated by the cyclic AMP receptor protein, CRP, that binds to the gal regulatory region and switches transcription from P2 to PI. With the point mutation, CRP binding swit- ches transcription from P3 to P1, although the formation of transcriptionally competent complexes at P1 is very slow. The results are discussed with respect to the mechanism of transcription activation by the CRP factor and the similarities between the regulatory regions of the galactose and lactose operons. -
Department of Health and Human Services National Institutes of Health
DEPARTMENT OF HEALTH AND HUMAN SERVICES NATIONAL INSTITUTES OF HEALTH RECOMBINANT DNA ADVISORY COMMITTEE MINUTES OF MEETING September 12-13, 1994 TABLE OF CONTENTS I. Call to Order/Dr. Walters II. Chair Report on Minor Modifications to NIH-Approved Human Gene Transfer Protocols/Dr. Walters III. Chair Report on Accelerated Review of Human Gene Transfer Protocols/Dr. Walters IV. Minutes of the June 9-10, 1994, Meeting V. Data Management Update/Dr. Smith VI. Discussion Regarding Criteria for RAC Review and Approval of Human Gene Transfer Protocols/Dr. Varmus VII. Addition to Appendix D of the NIH Guidelines Regarding a Human Gene Transfer Protocol Entitled: A Phase I Study of an Adeno-Associated Virus-CFTR Gene Vector in Adult CF Patients with MildLung Disease/Dr. Flotte VIII. Addition to Appendix D of the NIH Guidelines Regarding a Human Gene Transfer Protocol Entitled: Gene Therapy for the Treatment of Metastatic Breast Cancer by In Vivo Infection with Breast-Targeted Retroviral Vectors Expressing Antisense C-Fos or Antisense C-Myc RNA/Drs. Holt and Arteaga IX. Addition to Appendix D of the NIH Guidelines Regarding a HumanGene Transfer Protocol Entitled: Evaluation of Repeat Administrationof a Replication Deficient, Recombinant Adenovirus Containing the Normal Cystic Fibrosis Transmembrane Conductance Regulator cDNA to theAirways of Individuals with Cystic Fibrosis/Dr. Crystal X. Amendments to Sections I, III, IV, V, and Appendix M of theNIH Guidelines Regarding NIH and FDA Consolidated Review of Human Gene Transfer Protocols/Drs. Wivel and Noguchi XI. Addition to Appendix D of the NIH Guidelines Regarding a Human Gene Transfer Protocol Entitled: A Pilot Study of Autologous Human Interleukin-2 Gene Modified Tumor Cells in Patients with Refractory or Recurrent Metastatic Breast Cancer/Dr. -
Foundations of Biophysics and Structural Biology [GMS by 760]
Foundations of Biophysics And Structural Biology [GMS BY 760] Course Director: David Atkinson Ph.D. Professor of Physiology and Biophysics, Research Professor of Biochemistry Lecturers: Christopher W. Akey Ph.D. Professor of Physiology and Biophysics Olga Gursky Ph.D. Associate Professor of Physiology and Biophysics C. James McKnight Ph.D. Associate Professor of Physiology and Biophysics Michael Rynkiewicz Ph.D. Senior Research Associate in Physiology and Biophysics 1 COURSE INTRODUCTION ( David Atkinson Ph.D.) Lecture I. COURSE OVERVIEW Aims and organization, introduction to faculty, examinations, text books etc. MACROMOLECULAR CONFORMATION AND THE PRINCIPLES OF SYMMETRY Principles of symmetry, symmetry operations, point groups and space groups FOURIER TRANSFORMS (David Atkinson Ph.D.) Lecture I. FOURIER THEORY AND APPLICATION Waves, Fourier series. Fourier and inverse Fourier Transforms. 2 X-RAY DIFFRACTION, SCATTERING AND CRYSTALLOGRAPHY (Lectures I-III, David Atkinson Ph.D.,) (Lectures IV-VII. Michael Rynkiewicz Ph.D.) Lecture I. GEOMETRICAL DIFFRACTION Lattices, Unit Cells, Crystal Systems, Bragg’s Law, the Reciprocal Lattice, Space Groups, von Laue Conditions, Ewald sphere, Lecture II. FOURIER ANALYSIS Convolution and Correlation. Importance in structural biophysics. Lecture III. FOURIER ANALYSIS OF X-RAY SCATTERING AND DIFFRACTION Point scatterers, atomic scattering, form factors, assemblies of scatterers, lattices, electron density, Patterson function, resolution, phases and phase problem, symmetry and systematic absences. Lecture IV. PROTEIN CRYSTALLIZATION Preparing protein samples: Purification, concentrating, storage. Crystal growth: Principles and methods, solubility, saturation, nucleation, batch methods, vapor diffusion methods, dialysis methods, micro and macro seeding. Crystal storage and handling. Crystal soaking: Cryoprotectant, heavy atoms, substrates, ligands or inhibitors. Lecture V. MACROMOLECULAR DATA COLLECTION AND PROCESSING Data collection: Crystal mounting, radiation damage, cryo-techniques. -
Charles Robert Cantor (1942- ) [1]
Published on The Embryo Project Encyclopedia (https://embryo.asu.edu) Charles Robert Cantor (1942- ) [1] By: Abboud, Alexis Keywords: Sequenom [2] non-invasive prenatal genetic testing [3] Charles Robert Cantor helped sequence the human genome [4], and he developed methods to non-invasively determine the genes [5] in human fetuses. Cantor worked in the US during the twentieth and twenty-first centuries. His early research focused on oligonucleotides, small molecules of DNA or RNA. That research enabled the development of a technique that Cantor subsequently used to describe nucleotide sequences of DNA, a process called sequencing, in humans [6]. Cantor was the principal scientist for the Human Genome Project, for which scientists sequenced the entirety of the human genome [4] in 2003. Afterwards, Cantor became the chief scientific officer for Sequenom Inc., a company that provided non-invasive prenatal genetic testing. Such tests use a pregnant woman's blood to identify genetic mutations in a fetus [7] during the first trimester [8] of pregnancy [9]. Cantor was born on 26 August 1942 to Ida Dianne and Louis Cantor in Brooklyn, New York. As a high school student, he participated in a science program for high school seniors administered by Columbia University [10] in New York, New York. Afterwards, Cantor attended Columbia for his undergraduate degree. While there, Cantor took a course in population genetics taught by Richard Lewontin. Cantor later reported that the course and Lewontin influenced him to pursue biology. Cantor graduated from Columbia in 1963 with his degree. He then pursued doctoral studies in physical chemistry under Ignacio Tinoco Jr. -
OE Human Genome Program Second Contractor-Grantee Workshop (1991)
.. 1 II !I Acknowledgements I' I The. information for this report was compiled and prepared for publication by Laura Yust and other Human Genome Management Information System staff members. Charles Cantor contributed the I "Santa Fe Workshop Summary" with assistance from Elbert Branscomb, Anthony Carrano, Leroy Hood, Robert Moyzis, Robert Robbins, and DOE program staff. Sylvia Spengler (workshop organizer) and Eileen Mendez at the Lawrence Berkeley Laboratory Human Genome Center provided the abstracts. Most importantly, the contributions of grantees and contractors to the DOE Human Genome Program are gratefully acknowledged. For information or additional copies of this report contact: Laura Yust Human Genome Management Information System Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge, TN 37831-6050 615/574-7582, FrS 624-7582; Fax: 615/574-9888, FTS 624-9888; Internet: "[email protected]"; BITNET: "[email protected]" I I I This report has been reproduced directly from the best available copy. Available from the National Technical Information Service, U.S. Department of Commerce, Springfield, Virginia 22161. I -I Price: Printed Copy A06 II Microfiche AOl l l ' Codes are used for pricing all publications. The code is determined by the number of pages in the publication. Information pertaining to the pricing codes can be found in the current issues of the following publications, which are generally available in most libraries. Energy Research Abstracts, (ERA); Government Reports Announcements and Index (GRA and I); Scientific and Technical Abstract Reports (STAR); and publication, NTIS-PR-360 available from (NTIS) at the above address. Conf-91 02129 Dist: Category UC-408 DOE uman enome Program Report of the Second Contractor-Grantee Workshop February 17-20, 1991 Santa Fe, New Mexico Date Published: August 1991 Prepared for the U.S. -
Report of the 23Rd Asilomar Conference on Mass Spectrometry
Report of the 23rd Asilomar Conference on Mass Spectrometry Alan L. Rockwood ARUP Laboratories and Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA Ravinder J. Singh Mayo Clinic and Mayo Medical School, Rochester, Minnesota, USA ponsored by ASMS, the 2007 Asilomar conference mor marker) as a model of immunoassay imperfection. “Mass Spectrometry in Clinical Chemistry and Immunoassays are unreliable in some patients due to SMolecular Diagnostics” included 120 participants the presence of auto-antibodies that interfere with the from backgrounds as diverse as industry, instrumenta- test. Hoofnagle’s approach solves the problems of en- tion companies, hospitals, governmental laboratories, dogenous interfering antibodies (digest the sample into reference laboratories, medical schools, and other aca- peptides) and the lack of standardization between dif- demic institutions. The American Association for Clin- ferent commercial immunoassays (include an internal ical Chemistry accredited this conference for ACCENT standard peptide). continuing education credits. Christie Hunter from Applied Biosystems described Following opening comments by organizers Alan in “Peptide MRM-Based Assays in Plasma for Biomar- Rockwood and Ravinder Singh, Jack Henion from Ad- ker Verification Studies,” the use of a triple quadrupole vion Biosciences presented “Can Mass Spectrometry linear ion trap mass spectrometer to create more than Add Value to Modern Clinical Chemistry?” which 1000 high quality, specific MRM transitions for multiple overviewed the merits and issues pertaining to imple- peptides to many human plasma proteins. A non- menting mass spectrometry (especially LC/MS) into isobaric chemical labeling strategy was employed to the modern clinical laboratory. Strengths and limita- create global reference standards to enable quantitative tions of mass spectrometry were described, emphasiz- analysis. -
Boston University Graduate Program in Bioinformatics Handbook 2012
1 Boston University Graduate Program in Bioinformatics Handbook 2012-2013 http://www.bu.edu/bioinformatics Department of Biochemistry (School of Medicine) Department of Biology (College of Arts and Sciences) Biomedical Engineering Department (College of Engineering) Department of Biostatistics (School of Public Health) Department of Chemistry (College of Arts and Sciences) Department of Computational Biomedicine (School of Medicine) Department of Computer Science (College of Arts and Sciences) Electrical and Computer Engineering Department (College of Engineering) Genetics and Genomics Department (School of Medicine) Department of Mathematics and Statistics (College of Arts and Sciences) Department of Medicine (School of Medicine) Department of Microbiology (School of Medicine) Department of Mechanical Engineering (College of Engineering) Molecular and Cell Biology (Goldman School of Dental Health) Department of Neurology (School of Medicine) Periodontology & Oral Biology (Goldman School of Dental Health) Department of Physics (College of Arts and Sciences) Pulmonary Medicine (School of Medicine) Systems Engineering Division (College of Engineering) Center for Computational Science Center for Advanced Biotechnology Center for Advanced Genomic Technology Last Updated: 10/11/12 2 Bioinformatics Faculty and Staff Faculty Director Thomas Tullius Director of Bioinformatics Associate Directors Gary Benson* Associate Director of IGERT Scott Mohr Administrative Director, Director of Graduate Studies Department of Biochemistry (BUSM) Joseph Zaia Professor Associate Director, Center for Biomedical Mass Spectrometry Department of Biology (CAS) Cynthia Bradham Assistant Professor Geoffrey M. Cooper Professor, Associate Dean of the Faculty, Natural Sciences John Finnerty Associate Professor Ulla Hansen Professor Edward Loechler Professor Kimberly McCall Associate Professor # Daniel Segre* Associate Professor Dean Tolan Professor David Waxman Professor Department of Biomedical Engineering (ENG) Charles Cantor* Professor, Director of Center for Advanced Biotechnology James J. -
Chapter 21 Operons: Fine Control of Bacterial Transcription
Chapter 21 Operons: Fine Control of Bacterial Transcription The E. coli genome contains over 3000 genes. Some of these are active all the time because their products are in constant demand. But some of them are turned off most of the time because their products are rarely needed. For example, the enzymes required for the metabolism of the sugar arabinose would be useful only when arabinose is present and when the organism’s favorite energy source, glucose, is absent. Such conditions are not common, so the genes encoding these enzymes are usually turned off. Why doesn’t the cell just leave all its genes on all the time, so the right enzymes are always there to take care of any eventuality? The reason is that gene expression is an expensive process. It takes a lot of energy to produce RNA and protein. In fact, if all of an E. coli cell’s genes were turned on all the time, production of RNAs and proteins would drain the cell of so much energy that it could not compete with more effi cient organisms. Thus, control of gene expression is essential to life. Gene regulation is the device to insure that proteins are synthesized in exactly the amounts they are needed and only when they are needed. Transcriptional regulation: gene expression is controlled by regulatory proteins Negative regulation: - A repressor protein inhibits transcription of a specific gene. - In this case, inducer (antagonist of the repressor) is needed to allow transcription. Positive regulation: - Activator works to increase the frequency of transcription of an gene (operon) Transcriptional regulation: gene expression is controlled by regulatory proteins Operons Operons and the resulting transcriptional regulation of gene expression permit prokaryotes to rapidly adapt to changes in the environment: new carbon sources, lack of an amino acid, etc. -
The Regulation of Transcription Initiation in Bacteria
Annual Reviews www.annualreviews.org/aronline Ann.Rev. Genet. 1985. 19:35547 Copyright© 1985 by AnnualReviews Inc. All rights reserved THE REGULATION OF TRANSCRIPTIONINITIATION IN BACTERIA William S. Reznikoff I, Deborah A. Siegele 2, Deborah W. Cowingz, and2 Carol A. Gross Departmentsof Biochemistry~ andBacteriology 2, Collegeof Agriculturaland Life Sciences, Universityof Wisconsin,Madison, Wisconsin 53706 CONTENTS INTRODUCTION..................................................................................... 355 PROMOTERSTRUCTURE ......................................................................... 356 THEREGULATION OF E~TM TRANSCRIPTIONINITIATION ............................ 360 NegativeRegulation of TranscriptionInitiation ............................................. 361 Positive Regulationof TranscriptionInitiation .............................................. 363 DNATopology Regulation of TranscriptionInitiation ...................................... 365 DNAModification and the Regulationof GeneExpression ............................... 366 MODIFICATION OF HOLOENZYMESTRUCTURE AND THE REGULATION OF GENEEXPRESSION ................................................................... 366 E. coil ~r7° .......................................................................................... 367 ~2 by University of Wisconsin - Madison on 03/29/07. For personal use only. The HeatShock Response and ~r ............................................................. 368 The E. coli ntrA (glnF) Protein: AnotherSigma Factor ..................................