Mrna Secondary Structure Stability Regulates Bacterial Translation Insulation and Re-Initiation
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Downloaded from genome.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Research Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch Angel Carlos Roma´n,1 Francisco J. Gonza´lez-Rico,1 Eduardo Molto´,2,3 Henar Hernando,4 Ana Neto,5 Cristina Vicente-Garcia,2,3 Esteban Ballestar,4 Jose´ L. Go´mez-Skarmeta,5 Jana Vavrova-Anderson,6 Robert J. White,6,7 Lluı´s Montoliu,2,3 and Pedro M. Ferna´ndez-Salguero1,8 1Departamento de Bioquı´mica y Biologı´a Molecular, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain; 2Centro Nacional de Biotecnologı´a (CNB), Consejo Superior de Investigaciones Cientı´ficas (CSIC), Department of Molecular and Cellular Biology, Campus de Cantoblanco, C/Darwin 3, 28049 Madrid, Spain; 3Centro de Investigacio´n Biome´dica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; 4Chromatin and Disease Group, Cancer Epigenetics and Biology Programme, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona 08907, Spain; 5Centro Andaluz de Biologı´a del Desarrollo, CSIC-Universidad Pablo de Olavide, 41013 Sevilla, Spain; 6College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom; 7Beatson Institute for Cancer Research, Glasgow, G61 1BD, United Kingdom Complex genomes utilize insulators and boundary elements to help define spatial and temporal gene expression patterns. We report that a genome-wide B1 SINE (Short Interspersed Nuclear Element) retrotransposon (B1-X35S) has potent in- trinsic insulator activity in cultured cells and live animals. This insulation is mediated by binding of the transcription factors dioxin receptor (AHR) and SLUG (SNAI2) to consensus elements present in the SINE. -
Amino Acid Specificity in Translation
Opinion TRENDS in Biochemical Sciences Vol.30 No.12 December 2005 Amino acid specificity in translation Taraka Dale and Olke C. Uhlenbeck Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, IL 60208, USA Recent structural and biochemical experiments indicate For example, in the course of deducing the recognition that bacterial elongation factor Tu and the ribosomal rules of aaRSs, several amber-suppressor tRNA bodies A-site show specificity for both the amino acid and the were deliberately mutated such that they were amino- tRNA portions of their aminoacyl-tRNA (aa-tRNA) acylated by a different aaRS, and the resulting ‘identity- substrates. These data are inconsistent with the swapped’ tRNAs were shown to insert the new amino acid traditional view that tRNAs are generic adaptors in into protein [7,8]. In addition, suppressor tRNAs esterified translation. We hypothesize that each tRNA sequence with O30 different unnatural amino acids have been has co-evolved with its cognate amino acid, such that all successfully incorporated into protein [9]. Together, these aa-tRNAs are translated uniformly. data suggest that the translational apparatus lacks specificity for different amino acids, once they are Introduction esterified onto tRNA. The mechanism of protein synthesis is traditionally In a few isolated cases, however, the translation considered to have two phases with different specificities machinery seems to show specificity for the esterified towards the 20 amino acid side chains (Figure 1). In the amino acid. A prominent example occurs in the transami- first phase, each amino acid is specifically recognized by dation pathway, which is used as an alternative to GlnRS its cognate aminoacyl-tRNA synthetase (aaRS) and to produce Gln-tRNAGln in many bacteria and archaea esterified to the appropriate tRNA to form an aminoacyl- [10,11]. -
EF-Tu and Rnase E Are Functionally Connected
Till min familj List of Papers This thesis is based on the following papers, which are referred to in the text by their Roman numerals. I Hammarlöf, D.L., Hughes, D. (2008) Mutants of the RNA- processing enzyme RNase E reverse the extreme slow-growth phenotype caused by a mutant translation factor EF-Tu. Molecular Microbiology, 70(5), 1194-1209 II †Bergman, J., †Hammarlöf, D.L., Hughes D. (2011) Reducing ppGpp levels rescues the extreme growth defect of mutant EF-Tu. Manuscript III Hammarlöf, D.L., Liljas, L., Hughes, D. (2011) Temperature- sensitive mutants of RNase E in Salmonella enterica. Journal of Bacteriology. In press IV †Hammarlöf, D.L., †Bergman, J., Hughes, D. (2011) Extragenic suppressors of RNase E. Manuscript †These authors contributed equally. Reprints were made with permission from the respective publishers. Contents Introduction ................................................................................................... 11 Bacterial growth ....................................................................................... 11 Translation in bacteria .............................................................................. 12 The ribosome ....................................................................................... 12 The translation cycle ............................................................................ 13 Elongation Factor Tu ................................................................................ 14 The most abundant protein in the cell ................................................. -
Chromatin Insulators and Topological Domains: Adding New Dimensions to 3D Genome Architecture
Genes 2015, 6, 790-811; doi:10.3390/genes6030790 OPEN ACCESS genes ISSN 2073-4425 www.mdpi.com/journal/genes Review Chromatin Insulators and Topological Domains: Adding New Dimensions to 3D Genome Architecture Navneet K. Matharu 1,* and Sajad H. Ahanger 2,* 1 Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA 2 Department of Ophthalmology, Lab for Retinal Cell Biology, University of Zurich, Wagistrasse 14, Zurich 8952, Switzerland * Authors to whom correspondence should be addressed; E-Mails: [email protected] (N.K.M.); [email protected] (S.H.A.). Academic Editor: Jessica Tyler Received: 8 June 2015 / Accepted: 20 August 2015 / Published: 1 September 2015 Abstract: The spatial organization of metazoan genomes has a direct influence on fundamental nuclear processes that include transcription, replication, and DNA repair. It is imperative to understand the mechanisms that shape the 3D organization of the eukaryotic genomes. Chromatin insulators have emerged as one of the central components of the genome organization tool-kit across species. Recent advancements in chromatin conformation capture technologies have provided important insights into the architectural role of insulators in genomic structuring. Insulators are involved in 3D genome organization at multiple spatial scales and are important for dynamic reorganization of chromatin structure during reprogramming and differentiation. In this review, we will discuss the classical view and our renewed understanding of insulators as global genome organizers. We will also discuss the plasticity of chromatin structure and its re-organization during pluripotency and differentiation and in situations of cellular stress. -
Archaeal Translation Initiation Revisited: the Initiation Factor 2 and Eukaryotic Initiation Factor 2B ␣--␦ Subunit Families
Proc. Natl. Acad. Sci. USA Vol. 95, pp. 3726–3730, March 1998 Evolution Archaeal translation initiation revisited: The initiation factor 2 and eukaryotic initiation factor 2B a-b-d subunit families NIKOS C. KYRPIDES* AND CARL R. WOESE Department of Microbiology, University of Illinois at Urbana-Champaign, B103 Chemical and Life Sciences, MC 110, 407 S. Goodwin, Urbana, IL 61801 Contributed by Carl R. Woese, December 31, 1997 ABSTRACT As the amount of available sequence data bacterial and eukaryotic translation initiation mechanisms, increases, it becomes apparent that our understanding of although mechanistically generally similar, were molecularly translation initiation is far from comprehensive and that unrelated and so had evolved independently. The Methano- prior conclusions concerning the origin of the process are coccus jannaschii genome (7–9), which gave us our first wrong. Contrary to earlier conclusions, key elements of trans- comprehensive look at the componentry of archaeal transla- lation initiation originated at the Universal Ancestor stage, for tion initiation, revealed that archaeal translation initiation homologous counterparts exist in all three primary taxa. showed considerable homology with eukaryotic initiation, Herein, we explore the evolutionary relationships among the which, if anything, reinforced the divide between bacterial components of bacterial initiation factor 2 (IF-2) and eukary- initiation and that seen in the other domains. We recently have otic IF-2 (eIF-2)/eIF-2B, i.e., the initiation factors involved in shown, however, that bacterial translation initiation factor 1 introducing the initiator tRNA into the translation mecha- (IF-1), contrary to previously accepted opinion, is related in nism and performing the first step in the peptide chain sequence to its eukaryotic/archaeal (functional) counterpart, elongation cycle. -
Initiation Factor Eif5b Catalyzes Second GTP-Dependent Step in Eukaryotic Translation Initiation
Initiation factor eIF5B catalyzes second GTP-dependent step in eukaryotic translation initiation Joon H. Lee*†, Tatyana V. Pestova†‡§, Byung-Sik Shin*, Chune Cao*, Sang K. Choi*, and Thomas E. Dever*¶ *Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2716; ‡Department of Microbiology and Immunology, State University of New York Health Science Center, Brooklyn, NY 11203; and §A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia Edited by Harry F. Noller, University of California, Santa Cruz, CA, and approved October 31, 2002 (received for review September 19, 2002) Initiation factors IF2 in bacteria and eIF2 in eukaryotes are GTPases In addition, when nonhydrolyzable GDPNP was substituted Met that bind Met-tRNAi to the small ribosomal subunit. eIF5B, the for GTP, eIF5B catalyzed subunit joining; however, the factor eukaryotic ortholog of IF2, is a GTPase that promotes ribosomal was unable to dissociate from the 80S ribosome after subunit subunit joining. Here we show that eIF5B GTPase activity is re- joining (7). quired for protein synthesis. Mutation of the conserved Asp-759 in To dissect the function of the eIF5B G domain and test the human eIF5B GTP-binding domain to Asn converts eIF5B to an model that two GTP molecules are required in translation XTPase and introduces an XTP requirement for subunit joining and initiation, we mutated conserved residues in the eIF5B G translation initiation. Thus, in contrast to bacteria where the single domain and tested the function of the mutant proteins in GTPase IF2 is sufficient to catalyze translation initiation, eukaryotic translation initiation. -
Molecular Basis of the Function of Transcriptional Enhancers
cells Review Molecular Basis of the Function of Transcriptional Enhancers 1,2, 1, 1,3, Airat N. Ibragimov y, Oleg V. Bylino y and Yulii V. Shidlovskii * 1 Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; [email protected] (A.N.I.); [email protected] (O.V.B.) 2 Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia 3 I.M. Sechenov First Moscow State Medical University, 8, bldg. 2 Trubetskaya St., 119048 Moscow, Russia * Correspondence: [email protected]; Tel.: +7-4991354096 These authors contributed equally to this study. y Received: 30 May 2020; Accepted: 3 July 2020; Published: 5 July 2020 Abstract: Transcriptional enhancers are major genomic elements that control gene activity in eukaryotes. Recent studies provided deeper insight into the temporal and spatial organization of transcription in the nucleus, the role of non-coding RNAs in the process, and the epigenetic control of gene expression. Thus, multiple molecular details of enhancer functioning were revealed. Here, we describe the recent data and models of molecular organization of enhancer-driven transcription. Keywords: enhancer; promoter; chromatin; transcriptional bursting; transcription factories; enhancer RNA; epigenetic marks 1. Introduction Gene transcription is precisely organized in time and space. The process requires the participation of hundreds of molecules, which form an extensive interaction network. Substantial progress was achieved recently in our understanding of the molecular processes that take place in the cell nucleus (e.g., see [1–9]). -
A Subset of Drosophila Myc Sites Remain Associated with Mitotic Chromosomes Colocalized with Insulator Proteins
ARTICLE Received 16 Aug 2012 | Accepted 7 Jan 2013 | Published 12 Feb 2013 DOI: 10.1038/ncomms2469 A subset of Drosophila Myc sites remain associated with mitotic chromosomes colocalized with insulator proteins Jingping Yang1, Elizabeth Sung1, Paul G. Donlin-Asp1 & Victor G. Corces1 Myc has been characterized as a transcription factor that activates expression of genes involved in pluripotency and cancer, and as a component of the replication complex. Here we find that Myc is present at promoters and enhancers of Drosophila melanogaster genes during interphase. Myc colocalizes with Orc2, which is part of the prereplication complex, during G1. As is the case in mammals, Myc associates preferentially with paused genes, suggesting that it may also be involved in the release of RNA polymerase II from the promoter-proximal pausing in Drosophila. Interestingly, about 40% of Myc sites present in interphase persists during mitosis. None of the Myc mitotic sites correspond to enhancers, and only some correspond to promoters. The rest of the mitotic Myc sites overlap with binding sites for multiple insulator proteins that are also maintained in mitosis. These results suggest alternative mechanisms to explain the role of Myc in pluripotency and cancer. 1 Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA. Correspondence and requests for materials should be addressedto V.G.C. (email: [email protected]). NATURE COMMUNICATIONS | 4:1464 | DOI: 10.1038/ncomms2469 | www.nature.com/naturecommunications 1 & 2013 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms2469 yc has been extensively studied as an oncogene that has Results critical roles in cancer initiation and metastasis of many Myc is present at the promoters of paused genes. -
João Cancela De Amorim Falcão Paredes Estudo Molecular Da
Universidade de Aveiro Departamento de Biologia 2010 João Cancela de Estudo molecular da degeneração e evolução Amorim Falcão celular induzidas por erros na tradução do mRNA Paredes Molecular study of cell degeneration and evolution induced by mRNA mistranslation Universidade de Aveiro Departamento de Biologia 2010 João Cancela de Estudo molecular da degeneração e evolução Amorim Falcão celular induzidas por erros na tradução do mRNA Paredes Molecular study of cell degeneration and evolution induced by mRNA mistranslation Dissertação apresentada à Universidade de Aveiro para cumprimento dos requisitos necessários à obtenção do grau de Doutor em Biologia, realizada sob a orientação científica do Doutor Manuel António da Silva Santos, Professor Associado do Departamento de Biologia da Universidade de Aveiro. Apoio financeiro do POCI 2010 no âmbito do III Quadro Comunitário de Apoio, comparticipado pelo FSE e por fundos nacionais do MCES/FCT. “The known is finite, the unknown infinite; intellectually we stand on an islet in the midst of an illimitable ocean of inexplicability. Our business in every generation is to reclaim a little more land, to add something to the extent and the solidity of our possessions” Thomas Henry Huxley (1825 – 1895) o júri presidente Doutor Domingos Moreira Cardoso Professor Catedrático da Universidade de Aveiro Doutora Claudina Amélia Marques Rodrigues Pousada Professora Catedrática Convidada da Universidade Nova de Lisboa Doutor António Carlos Matias Correia Professor Catedrático da Universidade de Aveiro Doutor -
Genetic Insulator for Preventing Influence by Another Gene Promoter Susheng Gan University of Kentucky
University of Kentucky UKnowledge Plant and Soil Sciences Faculty Patents Plant and Soil Sciences 10-20-2009 Genetic Insulator for Preventing Influence by Another Gene Promoter Susheng Gan University of Kentucky Mingtang Xie Right click to open a feedback form in a new tab to let us know how this document benefits oy u. Follow this and additional works at: https://uknowledge.uky.edu/pss_patents Part of the Plant Sciences Commons Recommended Citation Gan, Susheng and Xie, Mingtang, "Genetic Insulator for Preventing Influence by Another Gene Promoter" (2009). Plant and Soil Sciences Faculty Patents. 35. https://uknowledge.uky.edu/pss_patents/35 This Patent is brought to you for free and open access by the Plant and Soil Sciences at UKnowledge. It has been accepted for inclusion in Plant and Soil Sciences Faculty Patents by an authorized administrator of UKnowledge. For more information, please contact [email protected]. US007605300B2 (12) United States Patent (10) Patent N0.: US 7,605,300 B2 Gan et al. (45) Date of Patent: Oct. 20, 2009 (54) GENETIC INSULATOR FOR PREVENTING Gan, S. Ph.D. Thesis; Molecular characterization and genetic INFLUENCE BY ANOTHER GENE manipulation of plant senescence (University of Wisconsin-Madi PROMOTER son, Madison, 1995).* Millar et al., The Plant Cell, vol. 11, pp. 825-838, May 1999. (75) Inventors: Susheng Gan, Lexington, KY (U S); NCBI, GenBank, AF129511, 2000. An G, “Binary Ti vectors for plant transformation and promoter Mingtang Xie, Burnaby (CA) analysis.” In Methods in Enzymology.‘ RecombinantDNA, R. Wu, and L. Grossman, eds, 292-305 (San Diego, Academic Press, 1987). (73) Assignee: University of Kentucky Research Bechtold N et al., “In Planta Agrobacterium-mediated gene transfer Foundation, Lexington, KY (U S) by in?ltration of adult Arabidopsis plants”, C R Acad Sci Paris 316, 1194-1199 (1993). -
Mitochondrial Translation and Beyond: Processes Implicated in Combined Oxidative Phosphorylation Deficiencies
Hindawi Publishing Corporation Journal of Biomedicine and Biotechnology Volume 2010, Article ID 737385, 24 pages doi:10.1155/2010/737385 Review Article Mitochondrial Translation and Beyond: Processes Implicated in Combined Oxidative Phosphorylation Deficiencies Paulien Smits, Jan Smeitink, and Lambert van den Heuvel Department of Pediatrics, Nijmegen Center for Mitochondrial Disorders, Radboud University Nijmegen Medical Center, Geert Grooteplein 10, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands Correspondence should be addressed to Lambert van den Heuvel, [email protected] Received 31 October 2009; Accepted 29 January 2010 Academic Editor: Aikaterini Kontrogianni-Konstantopoulos Copyright © 2010 Paulien Smits et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Mitochondrial disorders are a heterogeneous group of often multisystemic and early fatal diseases, which are amongst the most common inherited human diseases. These disorders are caused by defects in the oxidative phosphorylation (OXPHOS) system, which comprises five multisubunit enzyme complexes encoded by both the nuclear and the mitochondrial genomes. Due to the multitude of proteins and intricacy of the processes required for a properly functioning OXPHOS system, identifying the genetic defect that underlies an OXPHOS deficiency is not an easy task, especially in the case of combined OXPHOS defects. In the present communication we give an extensive overview of the proteins and processes (in)directly involved in mitochondrial translation and the biogenesis of the OXPHOS system and their roles in combined OXPHOS deficiencies. This knowledge is important for further research into the genetic causes, with the ultimate goal to effectively prevent and cure these complex and often devastating disorders. -
Open FINAL GRAD SCHOOL.Pdf
The Pennsylvania State University The Graduate School Eberly College of Science PHOSPHOPROTEOMIC ANALYSIS OF RIBOSOMAL PROTEINS: IMPLICATIONS IN TRANSLATION AND APOPTOSIS A Dissertation in Biochemistry, Microbiology, and Molecular Biology by Jennifer Lynn Miller © 2009 Jennifer Lynn Miller Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2009 The dissertation of Jennifer Lynn Miller was reviewed and approved* by the following: Emine C. Koc Assistant Professor Biochemistry and Molecular Biology Dissertation Advisor Chair of Committee Robert A. Schlegel Professor of Biochemistry and Molecular Biology Wendy Hanna-Rose Assistant Professor Biochemistry and Molecular Biology Ming Tien Professor of Biochemistry Erin D. Sheets Assistant Professor of Chemistry Richard J. Frisque Professor of Molecular Virology Head of the Department of Biochemistry and Molecular Biology *Signatures are on file in the Graduate School. ABSTRACT Mammalian mitochondrial ribosomes synthesize thirteen proteins that are essential for oxidative phosphorylation. Besides having a major role in ATP synthesis, mitochondria also contribute to biochemical processes coordinating apoptosis, mitochondrial diseases, and aging in eukaryotic cells. This unique class of ribosomes is protein-rich and distinct from cytoplasmic ribosomes. However, mitochondrial ribosomes (55S) share a significant homology to bacterial ribosomes (70S), particularly in size, the general mechanism of translation, and ribosomal protein content. Due to the overall resemblance between the two systems and the earlier reports of post-translational modifications, we investigated how phosphorylation of ribosomal proteins from bacteria and mitochondria regulates translation and other acquired roles. Identification of twenty- four phosphorylated 70S and 55S ribosomal proteins as well as the potential endogenous kinase was achieved using 2D-gel electrophoresis and tandem mass spectrometry.