Literature DB >> 32687319

Imaginary Ribozymes.

Ronald R Breaker1.   

Abstract

Biocatalysis is dominated by protein enzymes, and only a few classes of ribozymes are known to contribute to the task of promoting biochemical transformations. The RNA World theory encompasses the notion that earlier forms of life made use of a much greater diversity of ribozymes and other functional RNAs to guide complex metabolic states long before proteins had emerged in evolution. In recent years, the discoveries of various classes of ribozymes, riboswitches, and other noncoding RNAs in bacteria have provided additional support for the hypothesis that RNA molecules indeed have the catalytic competence to promote diverse chemical reactions without the aid of protein enzymes. Herein, some of the most striking observations made from examinations of natural riboswitches that bind small ligands are highlighted and used as a basis to imagine the characteristics and functions of long-extinct ribozymes from the RNA World.

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Year:  2020        PMID: 32687319      PMCID: PMC7919269          DOI: 10.1021/acschembio.0c00214

Source DB:  PubMed          Journal:  ACS Chem Biol        ISSN: 1554-8929            Impact factor:   5.100


  96 in total

1.  Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA.

Authors:  Brooke A Murphy McDaniel; Frank J Grundy; Irina Artsimovitch; Tina M Henkin
Journal:  Proc Natl Acad Sci U S A       Date:  2003-03-07       Impact factor: 11.205

Review 2.  The origins of the RNA world.

Authors:  Michael P Robertson; Gerald F Joyce
Journal:  Cold Spring Harb Perspect Biol       Date:  2012-05-01       Impact factor: 10.005

3.  Structure of the S-adenosylmethionine riboswitch regulatory mRNA element.

Authors:  Rebecca K Montange; Robert T Batey
Journal:  Nature       Date:  2006-06-29       Impact factor: 49.962

4.  Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis.

Authors:  Rüdiger Welz; Ronald R Breaker
Journal:  RNA       Date:  2007-02-16       Impact factor: 4.942

Review 5.  Guanidine-sensing riboswitches: How do they work and what do they regulate?

Authors:  Robert A Battaglia; Ailong Ke
Journal:  Wiley Interdiscip Rev RNA       Date:  2018-04-26       Impact factor: 9.957

6.  Structure of the SAM-II riboswitch bound to S-adenosylmethionine.

Authors:  Sunny D Gilbert; Robert P Rambo; Daria Van Tyne; Robert T Batey
Journal:  Nat Struct Mol Biol       Date:  2008-01-20       Impact factor: 15.369

7.  An excited state underlies gene regulation of a transcriptional riboswitch.

Authors:  Bo Zhao; Sharon L Guffy; Benfeard Williams; Qi Zhang
Journal:  Nat Chem Biol       Date:  2017-07-17       Impact factor: 15.040

8.  SAM-VI riboswitch structure and signature for ligand discrimination.

Authors:  Aiai Sun; Catherina Gasser; Fudong Li; Hao Chen; Stefan Mair; Olga Krasheninina; Ronald Micura; Aiming Ren
Journal:  Nat Commun       Date:  2019-12-16       Impact factor: 14.919

9.  Structure and ligand binding of the SAM-V riboswitch.

Authors:  Lin Huang; David M J Lilley
Journal:  Nucleic Acids Res       Date:  2018-07-27       Impact factor: 16.971

10.  Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine.

Authors:  Robert T Batey; Sunny D Gilbert; Rebecca K Montange
Journal:  Nature       Date:  2004-11-18       Impact factor: 49.962

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  9 in total

1.  An RNA aptamer that shifts the reduction potential of metabolic cofactors.

Authors:  John S Samuelian; Thomas J Gremminger; Zhenwei Song; Raghav R Poudyal; Jun Li; Yuanzhe Zhou; Seth A Staller; Johan A Carballo; Manami Roychowdhury-Saha; Shi-Jie Chen; Donald H Burke; Xiao Heng; Dana A Baum
Journal:  Nat Chem Biol       Date:  2022-09-12       Impact factor: 16.174

Review 2.  The case of the missing allosteric ribozymes.

Authors:  Shanker S S Panchapakesan; Ronald R Breaker
Journal:  Nat Chem Biol       Date:  2021-01-25       Impact factor: 15.040

3.  Thermal adaptation of structural dynamics and regulatory function of adenine riboswitch.

Authors:  Lin Wu; Zhijun Liu; Yu Liu
Journal:  RNA Biol       Date:  2021-02-25       Impact factor: 4.652

Review 4.  The Baltimore Classification of Viruses 50 Years Later: How Does It Stand in the Light of Virus Evolution?

Authors:  Eugene V Koonin; Mart Krupovic; Vadim I Agol
Journal:  Microbiol Mol Biol Rev       Date:  2021-07-14       Impact factor: 13.044

5.  Structure and mechanism of the methyltransferase ribozyme MTR1.

Authors:  Carolin P M Scheitl; Mateusz Mieczkowski; Hermann Schindelin; Claudia Höbartner
Journal:  Nat Chem Biol       Date:  2022-03-17       Impact factor: 16.174

Review 6.  An RNA-centric historical narrative around the Protein Data Bank.

Authors:  Eric Westhof; Neocles B Leontis
Journal:  J Biol Chem       Date:  2021-03-18       Impact factor: 5.157

7.  A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control.

Authors:  Griffin M Schroeder; Chapin E Cavender; Maya E Blau; Jermaine L Jenkins; David H Mathews; Joseph E Wedekind
Journal:  Nat Commun       Date:  2022-01-11       Impact factor: 17.694

8.  Structure and mechanism of a methyltransferase ribozyme.

Authors:  Jie Deng; Timothy J Wilson; Jia Wang; Xuemei Peng; Mengxiao Li; Xiaowei Lin; Wenjian Liao; David M J Lilley; Lin Huang
Journal:  Nat Chem Biol       Date:  2022-03-17       Impact factor: 16.174

9.  A natural riboswitch scaffold with self-methylation activity.

Authors:  Laurin Flemmich; Sarah Heel; Sarah Moreno; Kathrin Breuker; Ronald Micura
Journal:  Nat Commun       Date:  2021-06-23       Impact factor: 14.919

  9 in total

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