Control of Transcription Termination (DNA Sequencing/Attenuation/RNA Secondary Structure) JEFFREY F
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Mirnas and Lncrnas As Novel Therapeutic Targets to Improve Cancer Immunotherapy
cancers Review miRNAs and lncRNAs as Novel Therapeutic Targets to Improve Cancer Immunotherapy Maria Teresa Di Martino 1,*,† , Caterina Riillo 1,† , Francesca Scionti 2, Katia Grillone 1 , Nicoletta Polerà 1, Daniele Caracciolo 1, Mariamena Arbitrio 3, Pierosandro Tagliaferri 1 and Pierfrancesco Tassone 1 1 Department of Clinical and Experimental Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; [email protected] (C.R.); [email protected] (K.G.); [email protected] (N.P.); [email protected] (D.C.); [email protected] (P.T.); [email protected] (P.T.) 2 Institute of Research and Biomedical Innovation (IRIB), Italian National Council (CNR), 98164 Messina, Italy; [email protected] 3 Institute of Research and Biomedical Innovation (IRIB), Italian National Council (CNR), 88100 Catanzaro, Italy; [email protected] * Correspondence: [email protected] † These authors contributed equally. Simple Summary: Cancer onset and progression are promoted by high deregulation of the immune system. Recently, major advances in molecular and clinical cancer immunology have been achieved, offering new agents for the treatment of common tumors, often with astonishing benefits in terms of prolonged survival and even cure. Unfortunately, most tumors are still resistant to current immune therapy approaches, and basic knowledge of the resistance mechanisms is eagerly awaited. We Citation: Di Martino, M.T.; Riillo, C.; focused our attention on noncoding RNAs, a class of RNA that regulates many biological processes Scionti, F.; Grillone, K.; Polerà, N.; by targeting selectively crucial molecular pathways and that, recently, had their role in cancer cell Caracciolo, D.; Arbitrio, M.; immune escape and modulation of the tumor microenvironment identified, suggesting their function Tagliaferri, P.; Tassone, P. -
Recent Developments in Terminator Technology in Saccharomyces Cerevisiae
Journal of Bioscience and Bioengineering VOL. 128 No. 6, 655e661, 2019 www.elsevier.com/locate/jbiosc REVIEW Recent developments in terminator technology in Saccharomyces cerevisiae Takashi Matsuyama1 Toyota Central R&D Lab, Nagakute, Aichi 480-1192, Japan Received 20 March 2019; accepted 7 June 2019 Available online 16 July 2019 Metabolically engineered microorganisms that produce useful organic compounds will be helpful for realizing a sustainable society. The budding yeast Saccharomyces cerevisiae has high utility as a metabolic engineering platform because of its high fermentation ability, non-pathogenicity, and ease of handling. When producing yeast strains that produce exogenous compounds, it is a prerequisite to control the expression of exogenous enzyme-encoding genes. Terminator region in a gene expression cassette, as well as promoter region, could be used to improve metabolically engineered yeasts by increasing or decreasing the expression of the target enzyme-encoding genes. The findings on terminators have grown rapidly in the last decade, so an overview of these findings should provide a foothold for new developments. Ó 2019, The Society for Biotechnology, Japan. All rights reserved. [Key words: Terminator; Metabolic engineering; Genetic switch; Gene expression; Synthetic biology; Saccharomyces cerevisiae] In order to realize a sustainable society, many studies have been metabolic engineering, (iv) terminator selection for optimization of conducted to develop microorganisms that efficiently produce gene expression, (v) use of terminators as genetic switches, (vi) useful organic compounds using metabolic engineering (1). mechanism of action of highly active terminators and (vii) chal- Saccharomyces cerevisiae is considered to have high utility as a lenges in artificial terminator development. platform for these genetically-modified microorganisms for rea- sons such as high fermentation ability, high safety and easy BASIC FUNCTIONS OF THE TERMINATOR handling (2). -
Transcription Initiation Sites of the Leucine Operons of Salmonella Typhimurium and Escherichia Coli
J. Mol. Biol. (1983) 170, 39-59 Transcription Initiation Sites of the Leucine Operons of Salmonella typhimurium and Escherichia coli ROBERT M. GEMMILL~', JUDITH W. JONES, GEORGE W. HAUGHN AND JOSEPH M. CALVO Section of Biochemistry, Molecular and Cell Biology Cornell University, Ithaca, IV. Y. 14853, U.S.A. (Received 13 September 1982, and in revised form 15 June 1983) Evidence for a transcription attenuation site downstream from the leu promoter was obtained by transcription experiments in vitro. Most transcription initiated in vitro from teuP is terminated prematurely, resulting in the synthesis of a 160 nucleotide leader RNA. We define here the point at which transcription is initiated in vitro and in vivo and demonstrate that the site of premature termination is between the promoter and the first structural gene (leuA). Additional nucleotide sequences are presented that extend the known sequence 200 base-pairs upstream and 300 base-pairs downstream from leuP. The location of the promoter-proximal end of cistron leuA was deduced by comparing nucleotide sequence data with the sequence of the ten amino acids at the N-terminus of a-isopropylmalate synthase. To facilitate the isolation of quantities of material for sequencing experiments, the enzyme was isolated from a plasmid-containing strain, CV605, grown under conditions of leucine limitation. Under such conditions, about 20% of the total soluble protein of strain CV605 is a-isopropylmalate synthase and another 20~/o is fl-isopropylmalate dehydrogenase (leuB product). 1. Introduction Leucine biosynthesis in enteric bacteria is catalyzed by three enzymes whose levels are co-ordinately regulated by the intracellular concentration of leucine (Calvo et al., 1969a). -
Structural and Mechanistic Studies of the THI Box and SMK Box Riboswitches
Structural and Mechanistic Studies of the THI Box and SMK Box Riboswitches Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Angela Mae Smith, M.S. Graduate Program in Microbiology The Ohio State University 2009 Dissertation Committee: Professor Tina Henkin, Advisor Professor Kurt Fredrick Professor Michael Ibba Professor Ross Dalbey ABSTRACT Organisms have evolved a variety of mechanisms for regulating gene expression. Expression of individual genes is carefully modulated during different stages of cell development and in response to changing environmental conditions. A number of regulatory mechanisms involve structural elements within messenger RNAs (mRNAs) that, in response to an environmental signal, undergo a conformational change that affects expression of a gene encoded on that mRNA. RNA elements of this type that operate independently of proteins or translating ribosomes are termed riboswitches. In this work, the THI box and SMK box riboswitches were investigated in order to gain insight into the structural basis for ligand recognition and the mechanism of regulation employed by each of these RNAs. Both riboswitches are predicted to regulate at the level of translation initiation using a mechanism in which the Shine-Dalgarno (SD) sequence is occluded in response to ligand binding. For the THI box riboswitch, the studies presented here demonstrated that 30S ribosomal subunit binding at the SD region decreases in the presence of thiamin pyrophosphate (TPP). Mutation of conserved residues in the ligand binding domain resulted in loss of TPP-dependent repression in vivo. Based on these experiments two classes of mutant phenotypes were identified. -
Definition of RNA Polymerase II Cotc Terminator Elements in the Human
Cell Reports Article Definition of RNA Polymerase II CoTC Terminator Elements in the Human Genome Takayuki Nojima,1 Martin Dienstbier,2 Shona Murphy,1 Nicholas J. Proudfoot,1,* and Michael J. Dye1,* 1Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK 2MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, OX1 3QX Oxford, UK *Correspondence: [email protected] (N.J.P.), [email protected] (M.J.D.) http://dx.doi.org/10.1016/j.celrep.2013.03.012 SUMMARY ing and is entirely dependent upon the presence of a functional poly(A) signal (Whitelaw and Proudfoot, 1986; Connelly and Mammalian RNA polymerase II (Pol II) transcription Manley, 1988). Pre-mRNA cleavage at the poly(A) site, mediated termination is an essential step in protein-coding by the 30 end processing complex (Shi et al., 2009), generates 0 gene expression that is mediated by pre-mRNA pro- two RNA products; a 5 cleavage product that is stabilized by polyadenylation as it is processed into mRNA and a 30 cleavage cessing activities and DNA-encoded terminator ele- 0 0 ments. Although much is known about the role of product that is subject to rapid degradation by the 5 -3 exonu- pre-mRNA processing in termination, our under- clease Xrn2. Such Xrn2-mediated transcript degradation has been shown to have a role in Pol II termination (West et al., standing of the characteristics and generality of 2004). The above could lead one to conclude that the poly(A) terminator elements is limited. -
Terminator Operon Reporter: Combining a Transcription Termination Switch with Reporter Technology for Improved Gene Synthesis and Synthetic Biology Applications
www.nature.com/scientificreports OPEN Terminator Operon Reporter: combining a transcription termination switch with reporter Received: 02 March 2016 Accepted: 04 May 2016 technology for improved gene Published: 25 May 2016 synthesis and synthetic biology applications Massimiliano Zampini1, Luis A. J. Mur1, Pauline Rees Stevens1, Justin A. Pachebat1, C. James Newbold1, Finbarr Hayes2 & Alison Kingston-Smith1 Synthetic biology is characterized by the development of novel and powerful DNA fabrication methods and by the application of engineering principles to biology. The current study describes Terminator Operon Reporter (TOR), a new gene assembly technology based on the conditional activation of a reporter gene in response to sequence errors occurring at the assembly stage of the synthetic element. These errors are monitored by a transcription terminator that is placed between the synthetic gene and reporter gene. Switching of this terminator between active and inactive states dictates the transcription status of the downstream reporter gene to provide a rapid and facile readout of the accuracy of synthetic assembly. Designed specifically and uniquely for the synthesis of protein coding genes in bacteria, TOR allows the rapid and cost-effective fabrication of synthetic constructs by employing oligonucleotides at the most basic purification level (desalted) and without the need for costly and time-consuming post-synthesis correction methods. Thus, TOR streamlines gene assembly approaches, which are central to the future development of synthetic biology. Synthetic biology is an emerging discipline that aims to apply engineering principles to biology and has the poten- tial to drive a revolution in biotechnology1. The discipline has progressed particularly as a result of the implemen- tation of novel and powerful DNA construction techniques that allow for efficient assembly and manipulation of sequences both in vitro and in vivo2,3. -
Noncoding RNA E
Noncoding RNA E. Desgranges, S. Marzi, K. Moreau, P. Romby, Isabelle Caldelari To cite this version: E. Desgranges, S. Marzi, K. Moreau, P. Romby, Isabelle Caldelari. Noncoding RNA. Microbiology Spectrum, American Society for Microbiology, 2019, 7 (2), 10.1128/microbiolspec.GPP3-0038-2018. hal-02112074 HAL Id: hal-02112074 https://hal.archives-ouvertes.fr/hal-02112074 Submitted on 27 Oct 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Gram-positive pathogens, 3rd Edition (ASM) Staphylococcus section Chapter 5: non-coding RNA Desgranges, E. 1, Marzi, S. 1, Moreau, K. 2, Romby, P1, and Caldelari I1*. 1Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, F-67000 Strasbourg, France 2CIRI, International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, Univ Lyon, F-69008, Lyon, France *corresponding author General introduction Regulatory RNAs have been identified in many bacteria, and in pathogenic bacteria such as Staphylococcus aureus, where they play major roles in the regulation of virulence or metabolic proteins synthesis, beside transcriptional factors and two component systems (Bischoff and Romby, 2016, Tomasini et al., 2014, Guillet et al., 2013, Caldelari et al., 2011). -
The Arginine Attenuator Peptide Interferes with the Ribosome Peptidyl Transferase Center
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Texas A&M University The Arginine Attenuator Peptide Interferes with the Ribosome Peptidyl Transferase Center Jiajie Wei, Cheng Wu, and Matthew S. Sachs Department of Biology, Texas A&M University, College Station, Texas, USA The fungal arginine attenuator peptide (AAP) is encoded by a regulatory upstream open reading frame (uORF). The AAP acts as a nascent peptide within the ribosome tunnel to stall translation in response to arginine (Arg). The effect of AAP and Arg on ri- bosome peptidyl transferase center (PTC) function was analyzed in Neurospora crassa and wheat germ translation extracts using Downloaded from the transfer of nascent AAP to puromycin as an assay. In the presence of a high concentration of Arg, the wild-type AAP inhib- ited PTC function, but a mutated AAP that lacked stalling activity did not. While AAP of wild-type length was most efficient at stalling ribosomes, based on primer extension inhibition (toeprint) assays and reporter synthesis assays, a window of inhibitory function spanning four residues was observed at the AAP’s C terminus. The data indicate that inhibition of PTC function by the AAP in response to Arg is the basis for the AAP’s function of stalling ribosomes at the uORF termination codon. Arg could inter- fere with PTC function by inhibiting peptidyltransferase activity and/or by restricting PTC A-site accessibility. The mode of PTC inhibition appears unusual because neither specific amino acids nor a specific nascent peptide chain length was required for AAP to inhibit PTC function. -
Mutational Analysis of a Yeast Transcriptional Terminator (Linker Substitution/Saccharomyces Cerevisiae) BRIAN I
Proc. Natl. Acad. Sci. USA Vol. 86, pp. 4097-4101, June 1989 Cell Biology Mutational analysis of a yeast transcriptional terminator (linker substitution/Saccharomyces cerevisiae) BRIAN I. OSBORNE AND LEONARD GUARENTE Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 Communicated by S. E. Luria, January 23, 1989 ABSTRACT We have isolated and mutagenized a DNA scribed and 3' ends for both mRNAs fall within the 83-bp fragment from Saccharomyces cerevisiae that specifies mRNA region (Fig. 1). 3' end formation for the convergently transcribed CYCI and We showed previously that transcription of CYCJ-lacZ on UTRI genes. An in vivo plasmid supercoiling assay previously a plasmid in S. cerevisiae resulted in an increase in negative showed that this fragment is a transcriptional terminator, and supercoiling of the plasmid (27). By inserting the terminator "run-on" assays shown here are consistent with this interpre- fragment into various positions in CYCI-lacZ, we showed tation. The poly(A) sites in the mRNAs formed by the fragment that truncated transcripts of the expected sizes were gener- are the same whether the fragment resides at the native location ated, showing that the terminator fragment was sufficient to or at a heterologous location. No single linker substitution generate 3' ends. Further, the degree of relative, negative abolishes the fragment's activity, whereas certain large, supercoiling ofthese plasmids was proportional to the lengths nonoverlapping deletions have strong, deleterious effects. of truncated transcripts. We interpreted these changes in Therefore, the yeast terminator behaves more like rho- negative supercoiling as resulting from changes in the num- dependent bacterial terminators than terminators of higher bers of transcribing RNA polymerase molecules, suggesting eukaryotes. -
Facilitated Recycling Pathway for RNA Polymerase III
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Cell, Vol. 84, 245±252, January 26, 1996, Copyright 1996 by Cell Press Facilitated Recycling Pathway for RNA Polymerase III Giorgio Dieci* and Andre Sentenac exception of TFIID, and a new complex must be reas- Service de Biochimie et Ge ne tique Mole culaire sembled for each new cycle (Zawel et al., 1995). TFIID Commissariat aÁ l'Energie Atomique±Saclay remains promoter-bound through the transcription cycle F-91191 Gif-sur-Yvette Cedex and therefore facilitates reinitiation on the same tem- France plate (Hawley and Roeder, 1987; Jiang and Gralla, 1993). However, the release and reassociation of the other fac- tors make the reinitiation process more complex than Summary in the case of pol III and thus increase the number of critical checkpoints for transcriptional modulation. We show that the high in vitro transcription efficiency Some activators of pol II transcription have indeed been of yeast RNA pol III is mainly due to rapid recycling. shown to be required at each new cycle (Arnosti et al., Kinetic analysis shows that RNA polymerase recycling 1993; Roberts et al., 1995). Reinitiation on class III genes, on preassembled tDNA·TFIIIC·TFIIIB complexes is which bypasses almost all the steps required for the much faster than the initial transcription cycle. High initial transcription cycle, does not allow such a fine efficiency of RNA pol III recycling is favored at high regulation, but potentially leads to more efficient RNA UTP concentrations and requires termination at the production. -
Novel Mechanisms of Transcriptional Regulation by Leukemia Fusion Proteins
Novel mechanisms of transcriptional regulation by leukemia fusion proteins A dissertation submitted to the Graduate School of the University of Cincinnati in partial fulfillment of the requirement for the degree of Doctor of Philosophy in the Department of Cancer and Cell Biology of the College of Medicine by Chien-Hung Gow M.S. Columbia University, New York M.D. Our Lady of Fatima University B.S. National Yang Ming University Dissertation Committee: Jinsong Zhang, Ph.D. Robert Brackenbury, Ph.D. Sohaib Khan, Ph.D. (Chair) Peter Stambrook, Ph.D. Song-Tao Liu, Ph.D. ABSTRACT Transcription factors and chromatin structure are master regulators of homeostasis during hematopoiesis. Regulatory genes for each stage of hematopoiesis are activated or silenced in a precise, finely tuned manner. Many leukemia fusion proteins are produced by chromosomal translocations that interrupt important transcription factors and disrupt these regulatory processes. Leukemia fusion proteins E2A-Pbx1 and AML1-ETO involve normal function transcription factor E2A, resulting in two distinct types of leukemia: E2A-Pbx1 t(1;19) acute lymphoblastic leukemia (ALL) and AML1-ETO t(8;21) acute myeloid leukemia (AML). E2A, a member of the E-protein family of transcription factors, is a key regulator in hematopoiesis that recruits coactivators or corepressors in a mutually exclusive fashion to regulate its direct target genes. In t(1;19) ALL, the E2A portion of E2A-Pbx1 mediates a robust transcriptional activation; however, the transcriptional activity of wild-type E2A is silenced by high levels of corepressors, such as the AML1-ETO fusion protein in t(8;21) AML and ETO-2 in hematopoietic cells. -
Characterization of Transcriptional Control Elements in Cluster E Mycobacteriophage Ukulele
The University of Maine DigitalCommons@UMaine Honors College Spring 5-2016 Characterization of Transcriptional Control Elements in Cluster E Mycobacteriophage Ukulele Campbell Belisle Haley University of Maine Follow this and additional works at: https://digitalcommons.library.umaine.edu/honors Part of the Biochemistry Commons, and the Spanish Linguistics Commons Recommended Citation Haley, Campbell Belisle, "Characterization of Transcriptional Control Elements in Cluster E Mycobacteriophage Ukulele" (2016). Honors College. 397. https://digitalcommons.library.umaine.edu/honors/397 This Honors Thesis is brought to you for free and open access by DigitalCommons@UMaine. It has been accepted for inclusion in Honors College by an authorized administrator of DigitalCommons@UMaine. For more information, please contact [email protected]. CHARACTERIZATION OF TRANSCRIPTIONAL CONTROL ELEMENTS IN CLUSTER E MYCOBACTERIOPHAGE UKULELE By Campbell Belisle Haley Thesis Submitted in Partial Fulfillment of the Requirements for a Degree in Honors (Biochemistry and Spanish) The Honors College University of Maine May 2016 Advisory Committee: Sally D. Molloy, Advisor, Assistant Professor, Honors College and Department of Molecular and Biomedical Sciences Keith W. Hutchison, Professor Emeritus, Department of Molecular and Biomedical Sciences Melissa Maginnis, Assistant Professor, Department of Molecular and Biomedical Sciences Dorothy Croall, Professor, Department of Molecular and Biomedical Sciences David Gross, Adjunct Associate Professor in Honors Abstract Mycobacteriophage (phage) are a diverse group of viruses that infect Mycobacterium. Their study allows further understanding of viral evolution and genetics. Phage tightly control gene expression and transcribe their genes using host RNA polymerases. This project identifies potential transcriptional control elements in the genome of mycobacteriophage Ukulele. Promoters are sequences of the genome that allow binding of RNA polymerase and initiation of transcription.