Difference between revisions of "RNA switch"

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RNA switches may be triggered by proteins, tRNAs ([[T-box]]), or metabolites (riboswitches)
 
RNA switches may be triggered by proteins, tRNAs ([[T-box]]), or metabolites (riboswitches)
  
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==List of ''Bacillus subtilis'' RNAswitches==
+
==List of the ''Bacillus subtilis'' RNA switches==
  
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* Protein-dependent RNA switches
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* '''Protein-dependent RNA switches'''
 +
** [http://rfam.sanger.ac.uk/family?acc=RF00558 L20 leader]: in front of the ''[[infC]]-[[rpmI]]-[[rplT]]-[[ysdA]]'' operon: controlled by [[RplT]] binding
 +
** S4 leader: in front of the ''[[rpsD]]'' gene: controlled by ''RpsD'' binding
 +
** S15 leader: in front of the ''[[rpsO]]'' gene: controlled by ''RpsO'' binding
 +
** ''[[ptsG]]-[[ptsH]]-[[ptsI]]'': controlled by [[GlcT]]
 +
** ''[[sacX]]-[[sacY]]'', ''[[sacB]]'': controlled by [[SacY]]
 +
** ''[[sacP]]-[[sacA]]'': controlled by [[SacT]]
 +
** ''[[bglS]]'', ''[[bglP]]-[[bglH]]-[[yxiE]]'': controlled by [[LicT]]
 +
** ''[[glpD]]'', ''[[glpF]]-[[glpK]]'', ''[[glpT]]-[[glpQ]]'': controlled by [[GlpP]]
 +
** ''[[pabA]]'', ''[[trpE]]-[[trpD]]-[[trpC]]-[[trpF]]-[[trpB]]-[[trpA]]'', ''[[trpP]]'', ''[[ycbK]]'': controlled by [[MtrB|TRAP]]
 +
** ''[[hutH]]-[[hutU]]-[[hutI]]-[[hutG]]-[[hutM]]'': controlled by [[HutP]]
 +
** ''[[pyrR]]-[[pyrP]]-[[pyrB]]-[[pyrC]]-[[pyrAA]]-[[pyrAB]]-[[pyrK]]-[[pyrD]]-[[pyrF]]-[[pyrE]]'': controlled by [[PyrR]]
  
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*[[T-box]]
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*'''tRNA-dependent RNA switches: [[T-box]]'''
  
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* Riboswitches
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* '''Metabolite-dependent RNA switches: Riboswitches'''
 +
**[[A-box]]
 +
**[[B12 riboswitch]]
 
**[[FMN-box]]
 
**[[FMN-box]]
 
**[[G-box]]
 
**[[G-box]]
 +
**[[Gly-box]]
 +
**[[L-box]]
 
**[[M-box]]
 
**[[M-box]]
 
**[[preQ1 riboswitch]]
 
**[[preQ1 riboswitch]]
 
**[[ribozyme]]: ''[[glmS]]''
 
**[[ribozyme]]: ''[[glmS]]''
 
**[[S-box]]
 
**[[S-box]]
 +
**[[Thi-box]]
 +
**[[YdaO riboswitch]]
 +
**[[YkkC riboswitch]]: ''[[ykkC]]-[[ykkD]], [[yxkD]]''
 +
**[[yybP-ykoY motif]]: ''[[yybP]]'', ''[[ykoY]]''
 +
 +
* '''Additional RNA switches'''
 +
** ''[[pyrG]]'' RNA switch: low levels of intracellular CTP induce reiterative addition of G residues at position +4 in the 5' end of the ''[[pyrG]]'' mRNA, which is encoded as pppGGGC. . . . The poly(G) sequences formed under these conditions act to prevent attenuation by base pairing with the C- and U-rich 5' strand of a downstream terminator stem-loop located in the ''[[pyrG]]'' leader. {{PubMed|17302819}}
 +
** EAR (eps-associated RNA switch): located between'' [[epsB]]'' and ''[[epsC]]'', mediates  processive antitermination and allows expression of the long eps operon {{PubMed|20374491}}
 +
 +
The function of the following potential RNA structures is unknown. They were suggested to control the mentioned genes.
 +
** ''[[yjdF]]'' switch: ''[[yjdF]]'' {{PubMed|20230605}}
 +
** [http://rfam.sanger.ac.uk/family?acc=RF00516 ylbH switch]: ''[[ylbH]]''
 +
** [http://rfam.sanger.ac.uk/family?acc=RF00557 L10 leader]: ''[[rplJ]]''
 +
** [http://rfam.sanger.ac.uk/family?acc=RF00555 L13 leader]: ''[[rplM]]''
 +
** L19 leader: ''[[rplS]]''
 +
** [http://rfam.sanger.ac.uk/family?acc=RF00559 L21_leader]:in front of the ''[[rplU]]-[[ysxB]]-[[rpmA]]'' operon
 +
 +
* RNA switch candidates {{PubMed|20525796}}, upstream of:
 +
** ''[[clpX]]''
 +
** ''[[rpoB]]''
 +
** ''[[pdhA]]''
 +
** ''[[citZ]]''
 +
** ''[[yybN]]''
 +
** ''[[cwlO]]''
 +
** ''[[yxjJ]]''
 +
** ''[[ylxS]]''
 +
** ''[[ycdA]]''
 +
** ''[[tig]]''
 +
** ''[[ydbN]]''
 +
** ''[[rny]]''
 +
** ''[[yhdT]]''
 +
** ''[[ypfD]]''
 +
** ''[[sodA]]''
 +
** ''[[spoVS]]''
 +
** ''[[ylbK]]''
 +
** ''[[tagD]]''
 +
** ''[[yybS]]''
 +
** ''[[rplK]]''
 +
** ''[[fbaA]]''
 +
** ''[[dhbA]]''
 +
** ''[[yuxN]]''
 +
** ''[[rplU]]''
 +
** ''[[rpmH]]''
 +
** ''[[rex]]''
 +
** ''[[pelC]]''
 +
** ''[[yxbB]]''
 +
 +
==[http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb130_1.html An overview on the structural aspects]==
 +
==Important Original Publications==
 +
<pubmed> 24971878 27120414  28541183 37409574 </pubmed>
  
 
==Important Reviews==
 
==Important Reviews==
−
 
+
<pubmed>15063848 , 19385727 19250859 ,19141470 , 17092822, 17764952 ,17381303, 16226486 , 16153177 , 15750802, 14523920  18430893 12029388 19859665 19298181 20230605 20384681 12787499 14698618 21317561 21477128 21334966 20525796 21317561 23332744    27607554, 38385150
−
<pubmed>19250859 ,17764952 ,17381303, 16226486 , 16153177 , 15750802, 14523920  </pubmed>
+
</pubmed>

Latest revision as of 10:16, 23 February 2024

RNA switches are regulatory systems that rely on alternative mRNA structures.

RNA switches may be triggered by proteins, tRNAs (T-box), or metabolites (riboswitches)

List of the Bacillus subtilis RNA switches

  • tRNA-dependent RNA switches: T-box
  • Additional RNA switches
    • pyrG RNA switch: low levels of intracellular CTP induce reiterative addition of G residues at position +4 in the 5' end of the pyrG mRNA, which is encoded as pppGGGC. . . . The poly(G) sequences formed under these conditions act to prevent attenuation by base pairing with the C- and U-rich 5' strand of a downstream terminator stem-loop located in the pyrG leader. PubMed
    • EAR (eps-associated RNA switch): located between epsB and epsC, mediates processive antitermination and allows expression of the long eps operon PubMed

The function of the following potential RNA structures is unknown. They were suggested to control the mentioned genes.

An overview on the structural aspects

Important Original Publications

Jasleen Kaur Bains, Nusrat Shahin Qureshi, Betül Ceylan, Anna Wacker, Harald Schwalbe
Cell-free transcription-translation system: a dual read-out assay to characterize riboswitch function.
Nucleic Acids Res: 2023, 51(15);e82
[PubMed:37409574] [WorldCat.org] [DOI] (I p)

Hannah Steinert, Florian Sochor, Anna Wacker, Janina Buck, Christina Helmling, Fabian Hiller, Sara Keyhani, Jonas Noeske, Steffen Grimm, Martin M Rudolph, Heiko Keller, Rachel Anne Mooney, Robert Landick, Beatrix Suess, Boris Fürtig, Jens Wöhnert, Harald Schwalbe
Pausing guides RNA folding to populate transiently stable RNA structures for riboswitch-based transcription regulation.
Elife: 2017, 6;
[PubMed:28541183] [WorldCat.org] [DOI] (I e)

Daniel Dar, Maya Shamir, J R Mellin, Mikael Koutero, Noam Stern-Ginossar, Pascale Cossart, Rotem Sorek
Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria.
Science: 2016, 352(6282);aad9822
[PubMed:27120414] [WorldCat.org] [DOI] (I p)

Christopher J Robinson, Helen A Vincent, Ming-Cheng Wu, Phillip T Lowe, Mark S Dunstan, David Leys, Jason Micklefield
Modular riboswitch toolsets for synthetic genetic control in diverse bacterial species.
J Am Chem Soc: 2014, 136(30);10615-24
[PubMed:24971878] [WorldCat.org] [DOI] (I p)


Important Reviews

Anqi Peng, Guobin Yin, Wenjie Zuo, Luyao Zhang, Guocheng Du, Jian Chen, Yang Wang, Zhen Kang
##Title##
Synth Syst Biotechnol: 2024, 9(2);223-233
[PubMed:38385150] [WorldCat.org] [DOI] (I e)

Anna V Sherwood, Tina M Henkin
Riboswitch-Mediated Gene Regulation: Novel RNA Architectures Dictate Gene Expression Responses.
Annu Rev Microbiol: 2016, 70;361-74
[PubMed:27607554] [WorldCat.org] [DOI] (I p)

Alexander Serganov, Evgeny Nudler
A decade of riboswitches.
Cell: 2013, 152(1-2);17-24
[PubMed:23332744] [WorldCat.org] [DOI] (I p)

Laurène Bastet, Audrey Dubé, Eric Massé, Daniel A Lafontaine
New insights into riboswitch regulation mechanisms.
Mol Microbiol: 2011, 80(5);1148-54
[PubMed:21477128] [WorldCat.org] [DOI] (I p)

Charles L Turnbough
Regulation of gene expression by reiterative transcription.
Curr Opin Microbiol: 2011, 14(2);142-7
[PubMed:21334966] [WorldCat.org] [DOI] (I p)

Michelle M Meyer, Ming C Hammond, Yasmmyn Salinas, Adam Roth, Narasimhan Sudarsan, Ronald R Breaker
Challenges of ligand identification for riboswitch candidates.
RNA Biol: 2011, 8(1);5-10
[PubMed:21317561] [WorldCat.org] [DOI] (I p)

Irnov Irnov, Cynthia M Sharma, Jörg Vogel, Wade C Winkler
Identification of regulatory RNAs in Bacillus subtilis.
Nucleic Acids Res: 2010, 38(19);6637-51
[PubMed:20525796] [WorldCat.org] [DOI] (I p)

Irina Artsimovitch
A processive riboantiterminator seeks a switch to make biofilms.
Mol Microbiol: 2010, 76(3);535-9
[PubMed:20384681] [WorldCat.org] [DOI] (I p)

Zasha Weinberg, Joy X Wang, Jarrod Bogue, Jingying Yang, Keith Corbino, Ryan H Moy, Ronald R Breaker
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes.
Genome Biol: 2010, 11(3);R31
[PubMed:20230605] [WorldCat.org] [DOI] (I p)

Pascale Romby, Emmanuelle Charpentier
An overview of RNAs with regulatory functions in gram-positive bacteria.
Cell Mol Life Sci: 2010, 67(2);217-37
[PubMed:19859665] [WorldCat.org] [DOI] (I p)

Paul Babitzke, Carol S Baker, Tony Romeo
Regulation of translation initiation by RNA binding proteins.
Annu Rev Microbiol: 2009, 63;27-44
[PubMed:19385727] [WorldCat.org] [DOI] (I p)

Adam Roth, Ronald R Breaker
The structural and functional diversity of metabolite-binding riboswitches.
Annu Rev Biochem: 2009, 78;305-34
[PubMed:19298181] [WorldCat.org] [DOI] (I p)

Michael D Dambach, Wade C Winkler
Expanding roles for metabolite-sensing regulatory RNAs.
Curr Opin Microbiol: 2009, 12(2);161-9
[PubMed:19250859] [WorldCat.org] [DOI] (I p)

Tina M Henkin
Riboswitch RNAs: using RNA to sense cellular metabolism.
Genes Dev: 2008, 22(24);3383-90
[PubMed:19141470] [WorldCat.org] [DOI] (P p)

Jesse C Cochrane, Scott A Strobel
Riboswitch effectors as protein enzyme cofactors.
RNA: 2008, 14(6);993-1002
[PubMed:18430893] [WorldCat.org] [DOI] (I p)

Catherine A Wakeman, Wade C Winkler, Charles E Dann
Structural features of metabolite-sensing riboswitches.
Trends Biochem Sci: 2007, 32(9);415-24
[PubMed:17764952] [WorldCat.org] [DOI] (P p)

Irnov, A Kertsburg, W C Winkler
Genetic control by cis-acting regulatory RNAs in Bacillus subtilis: general principles and prospects for discovery.
Cold Spring Harb Symp Quant Biol: 2006, 71;239-49
[PubMed:17381303] [WorldCat.org] [DOI] (P p)

Frank J Grundy, Tina M Henkin
From ribosome to riboswitch: control of gene expression in bacteria by RNA structural rearrangements.
Crit Rev Biochem Mol Biol: 2006, 41(6);329-38
[PubMed:17092822] [WorldCat.org] [DOI] (P p)

Wade C Winkler
Riboswitches and the role of noncoding RNAs in bacterial metabolic control.
Curr Opin Chem Biol: 2005, 9(6);594-602
[PubMed:16226486] [WorldCat.org] [DOI] (P p)

Wade C Winkler, Ronald R Breaker
Regulation of bacterial gene expression by riboswitches.
Annu Rev Microbiol: 2005, 59;487-517
[PubMed:16153177] [WorldCat.org] [DOI] (P p)

Wade C Winkler
Metabolic monitoring by bacterial mRNAs.
Arch Microbiol: 2005, 183(3);151-9
[PubMed:15750802] [WorldCat.org] [DOI] (P p)

Frank J Grundy, Tina M Henkin
Regulation of gene expression by effectors that bind to RNA.
Curr Opin Microbiol: 2004, 7(2);126-31
[PubMed:15063848] [WorldCat.org] [DOI] (P p)

Alexey G Vitreschak, Dimitry A Rodionov, Andrey A Mironov, Mikhail S Gelfand
Riboswitches: the oldest mechanism for the regulation of gene expression?
Trends Genet: 2004, 20(1);44-50
[PubMed:14698618] [WorldCat.org] [DOI] (P p)

Wade C Winkler, Ronald R Breaker
Genetic control by metabolite-binding riboswitches.
Chembiochem: 2003, 4(10);1024-32
[PubMed:14523920] [WorldCat.org] [DOI] (P p)

Maumita Mandal, Benjamin Boese, Jeffrey E Barrick, Wade C Winkler, Ronald R Breaker
Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria.
Cell: 2003, 113(5);577-86
[PubMed:12787499] [WorldCat.org] [DOI] (P p)

Jörg Stülke
Control of transcription termination in bacteria by RNA-binding proteins that modulate RNA structures.
Arch Microbiol: 2002, 177(6);433-40
[PubMed:12029388] [WorldCat.org] [DOI] (P p)

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