Literature DB >> 23332744

A decade of riboswitches.

Alexander Serganov1, Evgeny Nudler.   

Abstract

Riboswitches were discovered in 2002 in bacteria as RNA-based intracellular sensors of vitamin derivatives. During the last decade, naturally occurring RNA sensor elements have been found to bind a range of small metabolites and ions and to exert regulatory control of transcription, translation, splicing, and RNA stability. Extensive biochemical, structural, and genetic studies have established the basic principles underpinning riboswitch function in all three kingdoms of life with implications for developing antibiotics, designing new molecular sensors, and integrating riboswitches into synthetic circuits.
Copyright © 2013 Elsevier Inc. All rights reserved.

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Year:  2013        PMID: 23332744      PMCID: PMC4215550          DOI: 10.1016/j.cell.2012.12.024

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   41.582


  82 in total

1.  Inducible gene expression from the plastid genome by a synthetic riboswitch.

Authors:  Andreas Verhounig; Daniel Karcher; Ralph Bock
Journal:  Proc Natl Acad Sci U S A       Date:  2010-03-22       Impact factor: 11.205

2.  Reengineering orthogonally selective riboswitches.

Authors:  Neil Dixon; John N Duncan; Torsten Geerlings; Mark S Dunstan; John E G McCarthy; David Leys; Jason Micklefield
Journal:  Proc Natl Acad Sci U S A       Date:  2010-01-26       Impact factor: 11.205

3.  Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch.

Authors:  Lili Huang; Alexander Serganov; Dinshaw J Patel
Journal:  Mol Cell       Date:  2010-12-10       Impact factor: 17.970

4.  Free state conformational sampling of the SAM-I riboswitch aptamer domain.

Authors:  Colby D Stoddard; Rebecca K Montange; Scott P Hennelly; Robert P Rambo; Karissa Y Sanbonmatsu; Robert T Batey
Journal:  Structure       Date:  2010-07-14       Impact factor: 5.006

5.  Reprogramming bacteria to seek and destroy an herbicide.

Authors:  Joy Sinha; Samuel J Reyes; Justin P Gallivan
Journal:  Nat Chem Biol       Date:  2010-05-09       Impact factor: 15.040

6.  Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways.

Authors:  Jérôme Mulhbacher; Eric Brouillette; Marianne Allard; Louis-Charles Fortier; François Malouin; Daniel A Lafontaine
Journal:  PLoS Pathog       Date:  2010-04-22       Impact factor: 6.823

7.  Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes.

Authors:  Zasha Weinberg; Joy X Wang; Jarrod Bogue; Jingying Yang; Keith Corbino; Ryan H Moy; Ronald R Breaker
Journal:  Genome Biol       Date:  2010-03-15       Impact factor: 13.583

8.  A pH-responsive riboregulator.

Authors:  Gal Nechooshtan; Maya Elgrably-Weiss; Abigail Sheaffer; Eric Westhof; Shoshy Altuvia
Journal:  Genes Dev       Date:  2009-11-15       Impact factor: 11.361

9.  A trans-acting riboswitch controls expression of the virulence regulator PrfA in Listeria monocytogenes.

Authors:  Edmund Loh; Olivier Dussurget; Jonas Gripenland; Karolis Vaitkevicius; Teresa Tiensuu; Pierre Mandin; Francis Repoila; Carmen Buchrieser; Pascale Cossart; Jörgen Johansson
Journal:  Cell       Date:  2009-11-13       Impact factor: 41.582

10.  An allosteric self-splicing ribozyme triggered by a bacterial second messenger.

Authors:  Elaine R Lee; Jenny L Baker; Zasha Weinberg; Narasimhan Sudarsan; Ronald R Breaker
Journal:  Science       Date:  2010-08-13       Impact factor: 47.728

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  384 in total

1.  Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation.

Authors:  Griffin M Schroeder; Debapratim Dutta; Chapin E Cavender; Jermaine L Jenkins; Elizabeth M Pritchett; Cameron D Baker; John M Ashton; David H Mathews; Joseph E Wedekind
Journal:  Nucleic Acids Res       Date:  2020-08-20       Impact factor: 16.971

2.  Role of lysine binding residues in the global folding of the lysC riboswitch.

Authors:  Erich Smith-Peter; Anne-Marie Lamontagne; Daniel A Lafontaine
Journal:  RNA Biol       Date:  2015       Impact factor: 4.652

3.  Selective small-molecule inhibition of an RNA structural element.

Authors:  John A Howe; Hao Wang; Thierry O Fischmann; Carl J Balibar; Li Xiao; Andrew M Galgoci; Juliana C Malinverni; Todd Mayhood; Artjohn Villafania; Ali Nahvi; Nicholas Murgolo; Christopher M Barbieri; Paul A Mann; Donna Carr; Ellen Xia; Paul Zuck; Dan Riley; Ronald E Painter; Scott S Walker; Brad Sherborne; Reynalda de Jesus; Weidong Pan; Michael A Plotkin; Jin Wu; Diane Rindgen; John Cummings; Charles G Garlisi; Rumin Zhang; Payal R Sheth; Charles J Gill; Haifeng Tang; Terry Roemer
Journal:  Nature       Date:  2015-09-30       Impact factor: 49.962

4.  Mg(2+) shifts ligand-mediated folding of a riboswitch from induced-fit to conformational selection.

Authors:  Krishna C Suddala; Jiarui Wang; Qian Hou; Nils G Walter
Journal:  J Am Chem Soc       Date:  2015-10-29       Impact factor: 15.419

5.  Nuclease-Resistant c-di-AMP Derivatives That Differentially Recognize RNA and Protein Receptors.

Authors:  Robert E Meehan; Chad D Torgerson; Barbara L Gaffney; Roger A Jones; Scott A Strobel
Journal:  Biochemistry       Date:  2016-02-03       Impact factor: 3.162

Review 6.  Themes and variations in riboswitch structure and function.

Authors:  Alla Peselis; Alexander Serganov
Journal:  Biochim Biophys Acta       Date:  2014-02-28

7.  Facile synthesis and evaluation of a dual-functioning furoyl probe for in-cell SHAPE.

Authors:  Dalen Chan; Samantha Beasley; Yuran Zhen; Robert C Spitale
Journal:  Bioorg Med Chem Lett       Date:  2018-02-01       Impact factor: 2.823

8.  sRNA-Mediated Control of Transcription Termination in E. coli.

Authors:  Nadezda Sedlyarova; Ilya Shamovsky; Binod K Bharati; Vitaly Epshtein; Jiandong Chen; Susan Gottesman; Renée Schroeder; Evgeny Nudler
Journal:  Cell       Date:  2016-09-22       Impact factor: 41.582

9.  Structural determinants for geometry and information decoding of tRNA by T box leader RNA.

Authors:  Jason C Grigg; Ailong Ke
Journal:  Structure       Date:  2013-10-03       Impact factor: 5.006

10.  Rational design of a synthetic mammalian riboswitch as a ligand-responsive -1 ribosomal frame-shifting stimulator.

Authors:  Ya-Hui Lin; Kung-Yao Chang
Journal:  Nucleic Acids Res       Date:  2016-08-12       Impact factor: 16.971

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