The Lac Operator-Repressor System Is Functional in the Mouse
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Galactosidase
Copyright 0 1988 by the Genetics Society of America Effects of Amino Acid Substitutions atthe Active Site in Escherichia coli @-Galactosidase Claire G. Cupples and Jeffrey H. Miller Molecular Biology Institute and Department of Biology, University of Calqornia, Los Angeles, Calqornia 90024 Manuscript received April 2 1, 1988 Accepted July 23, 1988 ABSTRACT Forty-nine amino acid substitutions were made at four positions in the Escherichia coli enzyme p- galactosidase; three of the four targeted amino acids are thought to be part of the active site. Many of the substitutions were made by converting the appropriate codon in lacZ to an amber codon, and using one of 12 suppressor strains to introduce the replacement amino acid. Glu-461 and Tyr-503 were replaced, independently, with 13 amino acids. All 26 of the strains containing mutant enzymes are Lac-. Enzyme activity is reduced to less than 10% of wild type by substitutions at Glu-461 and to less than 1% of wild type by substitutions at Tyr-503. Many of the mutant enzymes have less than 0.1 % wild-type activity. His-464 and Met-3 were replaced with 1 1and 12 amino acids, respectively. Strains containing any one of these mutant proteins are Lac+. The results support previous evidence that Glu-46 1 and Tyr-503 areessential for catalysis, and suggest that His-464 is not part of the active site. Site-directed mutagenesis was facilitated by construction of an fl bacteriophage containing the complete lacz gene on i single ECORIfragment. -GALACTOSIDASE (EC 3.2.1.23) is produced in and J. -
Reporter Genes a Practical Guide M E T H O D S I N M O L E C U L a R B I O L O G Y™
Reporter Genes A Practical Guide M E T H O D S I N M O L E C U L A R B I O L O G Y™ John M. Walker, SERIES EDITOR 436. Avian Influenza Virus, edited by 413. Protein Structure Prediction, Second Edition, Erica Spackman, 2008 edited by Mohammed Zaki and Chris Bystroff, 435. Chromosomal Mutagenesis, edited by 2008 Greg Davis and Kevin J. Kayser, 2008 412. Neutrophil Methods and Protocols, edited by 434. Gene Therapy Protocols: Vol. 2: Design and Mark T. Quinn, Frank R. DeLeo, Characterization of Gene Transfer Vectors, and Gary M. Bokoch, 2007 edited by Joseph M. LeDoux, 2008 411. Reporter Genes: A Practical Guide, edited by 433. Gene Therapy Protocols: Vol. 1: Production Don Anson, 2007 and In Vivo Applications of Gene Transfer 410. Environmental Genomics, edited by Vectors, edited by Joseph M. LeDoux, 2008 Cristofre C. Martin, 2007 432. Organelle Proteomics, edited by 409. Immunoinformatics: Predicting Immunogenicity Delphine Pflieger and Jean Rossier, 2008 In Silico, edited by Darren R. Flower, 2007 431. Bacterial Pathogenesis: Methods and 408. Gene Function Analysis, edited by Protocols, edited by Frank DeLeo and Michael Ochs, 2007 Michael Otto, 2008 407. Stem Cell Assays, edited by Vemuri C. Mohan, 430. Hematopoietic Stem Cell Protocols, 2007 edited by Kevin D. Bunting, 2008 406. Plant Bioinformatics: Methods and Protocols, 429. Molecular Beacons: Signalling Nucleic Acid edited by David Edwards, 2007 Probes, Methods and Protocols, edited by 405. Telomerase Inhibition: Strategies and Andreas Marx and Oliver Seitz, 2008 Protocols, edited by Lucy Andrews and 428. Clinical Proteomics: Methods and Protocols, Trygve O. -
Construction of a Copper Bioreporter Screening, Characterization and Genetic Improvement of Copper-Sensitive Bacteria
Construction of a Copper Bioreporter Screening, characterization and genetic improvement of copper-sensitive bacteria Puria Motamed Fath This thesis comprises 30 ECTS credits and is a compulsory part in the Master of Science With a Major in Industrial Biotechnology, 120 ECTS credits No. 9/2009 Construction of a Copper Bioreporter-Screening, characterization and genetic improvement of copper-sensitive bacteria Puria Motamed Fath, [email protected] Master thesis Subject Category: Technology University College of Borås School of Engineering SE-501 90 BORÅS Telephone +46 033 435 4640 Examiner: Dr. Elisabeth Feuk-lagerstedt Supervisor, name: Dr. Saman Hosseinkhani Supervisor, address: Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University Tehran, Iran Date: 2009-12-14 Keywords: Copper Bioreporter, Luciferase assay, COP operon, pGL3, E. Coli BL-21 ii Dedicated to my parents to whom I owe and feel the deepest gratitude iii Acknowledgment I would like to express my best appreciation to my supervisor Dr. S. Hosseinkhani for technical supports, and my examiner Dr. E. Feuk-lagerstedt for her kind attention, also I want to thank Mr. A. Emamzadeh, Miss. M. Nazari, and other students of Biochemistry laboratory of Tarbiat Modares University for their kind corporations. iv Abstract In the nature, lots of organism applies different kinds of lights such as flourescence or luminescence for some purposes such as defense or hunting. Firefly luciferase and Bacterial luciferase are the most famous ones which have been used to design Biosensors or Bioreporters in recent decades. Their applications are so extensive from detecting pollutions in the environment to medical and treatment usages. -
BMB400 Part Four - II = Chpt
BMB400 Part Four - II = Chpt. 17. Transcriptional regulation by effects on RNA polymerase B M B 400 Part Four: Gene Regulation Section II = Chapter 17. TRANSCRIPTIONAL REGULATION EXERTED BY EFFECTS ON RNA POLYMERASE [Dr. Tracy Nixon made major contributions to this chapter.] A. The multiple steps in initiation and elongation by RNA polymerase are targets for regulation. 1. RNA Polymerase has to * bind to promoters, * form an open complex, * initiate transcription, * escape from the promoter, * elongate , and * terminate transcription. See Fig. 4.2.1. 2. Summarizing a lot of work, we know that: • strong promoters have high KB, high kf, low kr, and high rates of promoter clearance. • weak promoters have low KB, low kf, high kr, and low rates of promoter clearance. • moderate promoters have one or more "weak" spots. 3. To learn these facts, we need: • genetic data to identify which macromolecules (DNA and proteins) interact in a specific regulation event, and to determine which base pairs and amino acid residues are needed for that regulation event. • biochemical data to describe the binding events and chemical reactions that are affected by the specific regulation event. Ideally, we would determine all forward and reverse rate constants, or equilibrium constants (which are a function of the ratio of rate constants) if rates are inaccessible. Although, in reality, we cannot get either rates or equilibrium constants for many of the steps, some of the steps are amenable to investigation and have proved to be quite informative about the mechanisms of regulation. BMB400 Part Four - II = Chpt. 17. Transcriptional regulation by effects on RNA polymerase Fig. -
Solutions for Practice Problems for Molecular Biology, Session 5
Solutions to Practice Problems for Molecular Biology, Session 5: Gene Regulation and the Lac Operon Question 1 a) How does lactose (allolactose) promote transcription of LacZ? 1) Lactose binds to the polymerase and increases efficiency. 2) Lactose binds to a repressor protein, and alters its conformation to prevent it from binding to the DNA and interfering with the binding of RNA polymerase. 3) Lactose binds to an activator protein, which can then help the RNA polymerase bind to the promoter and begin transcription. 4) Lactose prevents premature termination of transcription by directly binding to and bending the DNA. Solution: 2) Lactose binds to a repressor protein, and alters its conformation to prevent it from binding to the DNA and interfering with the binding of RNA polymerase. b) What molecule is used to signal low glucose levels to the Lac operon regulatory system? 1) Cyclic AMP 2) Calcium 3) Lactose 4) Pyruvate Solution: 1) Cyclic AMP. Question 2 You design a summer class where you recreate experiments studying the lac operon in E. coli (see schematic below). In your experiments, the activity of the enzyme b-galactosidase (β -gal) is measured by including X-gal and IPTG in the growth media. X-gal is a lactose analog that turns blue when metabolisize by b-gal, but it does not induce the lac operon. IPTG is an inducer of the lac operon but is not metabolized by b-gal. I O lacZ Plac Binding site for CAP Pi Gene encoding β-gal Promoter for activator protein Repressor (I) a) Which of the following would you expect to bind to β-galactosidase? Circle all that apply. -
Mechanism of Promoter Repression by Lac Repressor–DNA Loops Nicole A
156–166 Nucleic Acids Research, 2013, Vol. 41, No. 1 Published online 9 November 2012 doi:10.1093/nar/gks1011 Mechanism of promoter repression by Lac repressor–DNA loops Nicole A. Becker1, Justin P. Peters1, Troy A. Lionberger2 and L. James Maher III1,* 1Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street Southwest, Rochester, MN 55905, USA and 2Howard Hughes Medical Institute and Jason L. Choy Laboratory of Single-Molecule Biophysics, Department of Physics, University of California, Berkeley, CA 94720, USA Received June 29, 2012; Revised October 1, 2012; Accepted October 2, 2012 ABSTRACT presence of allolactose or its analog, isopropyl b-D-1- thiogalactopyranoside (IPTG), relieving repression. In the The Escherichia coli lactose (lac) operon encodes absence of glucose, RNA polymerase binds cooperatively the first genetic switch to be discovered, and lac with catabolite activator protein at the lac promoter (positive remains a paradigm for studying negative and control). In simplest terms, the mechanism of negative positive control of gene expression. Negative control involves Lac repressor binding to occlude access control is believed to involve competition of RNA of RNA polymerase holoenzyme to the lac promoter (4). polymerase and Lac repressor for overlapping Of particular significance to the present work is the binding sites. Contributions to the local Lac repres- fascinating observation that two remote auxiliary oper- sor concentration come from free repressor and re- ators (Oaux) exist in the lac operon (5). It has been pressor delivered to the operator from remote proposed and demonstrated (6–13) that bidentate repres- auxiliary operators by DNA looping. -
Reporter Gene Assays
TCA-017 Reporter Gene Assays Abstract foreign to mammalian cells, and are biologically active without post-translational modification. Luminescent reporter gene assays provide a simple, fast, non-isotopic, and highly sensitive alternative to The high quantum efficiency of luciferase enables the popular radioactive chloramphenicol detection of less than 0.01 attomoles of luciferase, acetyltransferase (CAT) assay. This paper describes making it possible to scale down the assay to the a reporter gene assay in which cells were transfected 96-well microplate format.1,2 Although the luciferin/ with the firefly luciferase gene, which was quanti- luciferase reaction is often thought of as a flash fied using an enhanced flash luciferin substrate chemistry, recent advances have extended the pho- and the TopCount Microplate Scintillation and ton kinetics by the use of coenzyme A as a substrate Luminescence Counter. Co-transfection with the in the oxidation of luciferin.3 The resulting enhanced ß-galactosidase gene may be included to control for flash eliminates the need for elaborate reagent inter-assay transfection efficiency. Both of these injection devices. luminescent reporters can be quantified without reagent injection devices. The signal decays only slightly during the time required to read a microplate, Co-transfection with a second reporter gene is often and can be easily corrected for the decay by tandem performed to normalize transfection efficiency processing on TopCount. between assays. The ß-galactosidase gene is ideal for this application. Chemiluminescent substrates for ß- galactosidase are sensitive enough to allow detec- Introduction tion at low transfection efficiency, are available in compatible plasmid vectors, and are easily adaptable The use of reporter genes is a fundamental tool of 4 molecular biologists. -
Important Vector Factors for Gene Expression Technical Reference Guide
BioResearch Important Vector Factors for Gene Expression Technical Reference Guide vectors expressing the same luciferase gene in different backbones and expression cassettes and obtained highly discriminative expres- sion levels. In this guideline, we show the most important aspects to be considered when choosing an expression vector and their impact on your experimental results. 1. Promoter Strength Introduction Is your promoter appropriate for the cell type that you are working with? Our Scientific Support Team is commonly asked: “Why don’t I get the Table 1 describes the promoter strengths as a relative percent of the same expression level of my gene if I use various vector backbones?” strength of the CMV promoter for various cells for which Lonza has There are many components to a vector that can have an effect on the Optimized Protocols. The CMV promoter activity is set to 100% based level of gene expression. Below you will find the 10 most important on their CAT assay values from the referenced publications. Although factors to consider when looking at vectors. CMV is a strong promoter in many mammalian cells, another promoter The selection of an appropriate expression vector is crucial for efficient may give stronger expression in your cells (e.g., promoter SV40 in gene expression. Just take a look at Figure 1. We tried 10 different BHK-21 cells). n 1600 1400 1200 1000 800 [% of pGL3-CMV at 24 h] 24 at pGL3-CMV [% of 600 400 Relative luciferase-expressio Relative 200 0 Control Program Only pGL3-Control pGL3-CMV pmax Cloning™ pSG5 pcDNA3.1 pFP pIRES-MCS B pcDNA4 HisMax pCMVbeta pCMV-TNT 4 hours 24 hours 48 hours n 2000 1500 1000 500 0 Control Program Only pGL3-Control pGL3-CMV pmax Cloning™ pSG5 pcDNA3.1 pFP pIRES-MCS B pcDNA4 HisMax pCMVbeta pCMV-TNT [% of pGL3-CMV at 24 h] 24 at pGL3-CMV [% of 4 hours 24 hours 48 hours Relative luciferase-expressio Relative Figure 1: Luciferase expression levels depend on vector backbones. -
Robust Normalization of Luciferase Reporter Data
Technical Note Robust Normalization of Luciferase Reporter Data Andrea Repele † and Manu * Department of Biology, University of North Dakota, Grand Forks, ND 58202, USA * Correspondence: [email protected] † Current address: JMB—Center for Immunity and Immunotherapies, Seattle Children’s Hospital, Seattle, WA 98105, USA. Received: 17 June 2019; Accepted: 22 July 2019; Published: 25 July 2019 Abstract: Transient Luciferase reporter assays are widely used in the study of gene regulation and intracellular cell signaling. In order to control for sample-to-sample variation in luminescence arising from variability in transfection efficiency and other sources, an internal control reporter is co-transfected with the experimental reporter. The luminescence of the experimental reporter is normalized against the control by taking the ratio of the two. Here we show that this method of normalization, “ratiometric”, performs poorly when the transfection efficiency is low and leads to biased estimates of relative activity. We propose an alternative methodology based on linear regression that is much better suited for the normalization of reporter data, especially when transfection efficiency is low. We compare the ratiometric method against three regression methods on both simulated and empirical data. Our results suggest that robust errors-in-variables (REIV) regression performs the best in normalizing Luciferase reporter data. We have made the R code for Luciferase data normalization using REIV available on GitHub. Keywords: luciferase reporter; transfection efficiency; normalization; gene regulation; promoter; enhancer 1. Introduction Transient reporter assays are an important and widely used tool in the study of gene regulation [1–4], intracellular cell signaling [5–7], and other areas of molecular, cellular, and developmental biology [8–10]. -
I = Chpt 15. Positive and Negative Transcriptional Control at Lac BMB
BMB 400 Part Four - I = Chpt 15. Positive and Negative Transcriptional Control at lac B M B 400 Part Four: Gene Regulation Section I = Chapter 15 POSITIVE AND NEGATIVE CONTROL SHOWN BY THE lac OPERON OF E. COLI A. Definitions and general comments 1. Operons An operon is a cluster of coordinately regulated genes. It includes structural genes (generally encoding enzymes), regulatory genes (encoding, e.g. activators or repressors) and regulatory sites (such as promoters and operators). 2. Negative versus positive control a. The type of control is defined by the response of the operon when no regulatory protein is present. b. In the case of negative control, the genes in the operon are expressed unless they are switched off by a repressor protein. Thus the operon will be turned on constitutively (the genes will be expressed) when the repressor in inactivated. c. In the case of positive control, the genes are expressed only when an active regulator protein, e.g. an activator, is present. Thus the operon will be turned off when the positive regulatory protein is absent or inactivated. Table 4.1.1. Positive vs. negative control BMB 400 Part Four - I = Chpt 15. Positive and Negative Transcriptional Control at lac 3. Catabolic versus biosynthetic operons a. Catabolic pathways catalyze the breakdown of nutrients (the substrate for the pathway) to generate energy, or more precisely ATP, the energy currency of the cell. In the absence of the substrate, there is no reason for the catabolic enzymes to be present, and the operon encoding them is repressed. In the presence of the substrate, when the enzymes are needed, the operon is induced or de-repressed. -
Tnlo-Encoded Tet Repressor Can Regulate an Operator-Containing
Proc. Nati. Acad. Sci. USA Vol. 85, pp. 1394-1397, March 1988 Biochemistry TnlO-encoded tet repressor can regulate an operator-containing plant promoter (cauliflower mosaic virus 35S promoter/electroporation/transient chloramphenicol acetyltransferase assays) CHRISTIANE GATZ* AND PETER H. QUAILt Departments of Botany and Genetics, University of Wisconsin, Madison, WI 53706 Communicated by Folke Skoog, October 26, 1987 (receivedfor review July S, 1987) ABSTRACT The TnlO-encoded tet repressor-operator The TnlO-encoded tet repressor regulates the expression system was used to regulate transcription from the cauliflower of the Tc resistance operon by binding to nearly identical mosaic virus (CaMV) 35S promoter. Expression was moni- operator sequences that overlap with three divergent pro- tored in a transient assay system by using electric field- moters (14, 15). The genes of the tet operon are only mediated gene transfer ("electroporation") into tobacco pro- transcribed in the presence of the inducer Tc, which pre- toplasts. The tet repressor, being expressed in the plant cells vents the repressor from binding to its operator sequences. under the control of eukaryotic transcription signals, blocks The tet repressor was chosen for regulating a plant promoter transcription of a CaMV 35S promoter chloramphenicol ace- for two reasons. (i) With a native molecular mass of 48 kDa, tyltransferase (cat) fusion gene when the two tet operators diffusion into the nucleus seemed likely (16). (ii) The high flank the "TATA" box. In the presence of the inducer equilibrium association constant of the repressor-inducer tetracycline, expression is restored to full activity. Location of complex ensures efficient induction at sublethal Tc concen- the operators 21 base pairs downstream of the transcription trations (17), thus making the system useful as an on/off start site does not significantly affect transcription in the switch for the specific regulation of transferred genes. -
Ab253372 Β-Glucuronidase (GUS) Reporter Gene Activity Detection Kit
Version 1 Last updated 14 June 2020 ab253372 β-Glucuronidase (GUS) Reporter Gene Activity Detection Kit View β-Glucuronidase (GUS) Reporter Gene Activity Detection Kit datasheet: www.abcam.com/ab253372 (use www.abcam.cn/ab253372 for China, or www.abcam.co.jp/ab253372 for Japan) For the measurement of β-Glucuronidase (GUS) activity in plant tissue. This product is for research use only and is not intended for diagnostic use. Copyright © 2020 Abcam. All rights reserved Table of Contents 1. Overview 1 2. Materials Supplied and Storage 2 3. Materials Required, Not Supplied 3 4. General guidelines, precautions, and troubleshooting 3 5. Reagent Preparation 4 6. Assay Procedure 5 7. Typical Data 7 8. Notes 9 Technical Support 10 Copyright © 2020 Abcam. All rights reserved 1. Overview Reporter genes are widely used as “markers” for analysis in gene regulation and localization, as well as for analysis of mutation altered genes. Expression of reporter genes can be measured by immunological assay, biochemical activity assay or by histochemical staining of cells or tissues. The β-glucuronidase (GUS) enzyme from E. coli (EC 3.2.1.31) has been well documented to provide desirable characteristics as a marker gene in transformed plants. The GUS reporter gene system has many advantages including stable expression of E. coli GUS enzyme, no interference with normal plant metabolism, and low intrinsic GUS activity in higher plants. The enzyme is also capable of tolerating amino-terminal additions, making it useful for study of plant organelle transport. Plants or other cell types are extracted with GUS extraction buffer. The extracted β-glucuronidase hydrolyzes the 4-MUG to the fluorescent compound 4-MU (pKa 8.2) and glucuronic acid.