Difference between revisions of "RNA switch"

From SubtiWiki
Jump to: navigation, search
(→‎Important Reviews)
(→‎Important Reviews)
 
(24 intermediate revisions by the same user not shown)
Line 3: Line 3:
 
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)
  
−
==List of ''Bacillus subtilis'' RNAswitches==
+
==List of the ''Bacillus subtilis'' RNA switches==
  
 
* '''Protein-dependent RNA switches'''
 
* '''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
 
** [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]]
 
** ''[[ptsG]]-[[ptsH]]-[[ptsI]]'': controlled by [[GlcT]]
 
** ''[[sacX]]-[[sacY]]'', ''[[sacB]]'': controlled by [[SacY]]
 
** ''[[sacX]]-[[sacY]]'', ''[[sacB]]'': controlled by [[SacY]]
 
** ''[[sacP]]-[[sacA]]'': controlled by [[SacT]]
 
** ''[[sacP]]-[[sacA]]'': controlled by [[SacT]]
−
** ''[[bglS]]'', ''[[bglP]]-[[bglH]]-[[yxiE]]'': controlled by [[BglP]]
+
** ''[[bglS]]'', ''[[bglP]]-[[bglH]]-[[yxiE]]'': controlled by [[LicT]]
 
** ''[[glpD]]'', ''[[glpF]]-[[glpK]]'', ''[[glpT]]-[[glpQ]]'': controlled by [[GlpP]]
 
** ''[[glpD]]'', ''[[glpF]]-[[glpK]]'', ''[[glpT]]-[[glpQ]]'': controlled by [[GlpP]]
 
** ''[[pabA]]'', ''[[trpE]]-[[trpD]]-[[trpC]]-[[trpF]]-[[trpB]]-[[trpA]]'', ''[[trpP]]'', ''[[ycbK]]'': controlled by [[MtrB|TRAP]]
 
** ''[[pabA]]'', ''[[trpE]]-[[trpD]]-[[trpC]]-[[trpF]]-[[trpB]]-[[trpA]]'', ''[[trpP]]'', ''[[ycbK]]'': controlled by [[MtrB|TRAP]]
Line 16: Line 18:
 
** ''[[pyrR]]-[[pyrP]]-[[pyrB]]-[[pyrC]]-[[pyrAA]]-[[pyrAB]]-[[pyrK]]-[[pyrD]]-[[pyrF]]-[[pyrE]]'': controlled by [[PyrR]]
 
** ''[[pyrR]]-[[pyrP]]-[[pyrB]]-[[pyrC]]-[[pyrAA]]-[[pyrAB]]-[[pyrK]]-[[pyrD]]-[[pyrF]]-[[pyrE]]'': controlled by [[PyrR]]
  
−
*'''[[T-box]]'''
+
*'''tRNA-dependent RNA switches: [[T-box]]'''
  
−
* '''Riboswitches'''
+
* '''Metabolite-dependent RNA switches: Riboswitches'''
 
**[[A-box]]
 
**[[A-box]]
 +
**[[B12 riboswitch]]
 
**[[FMN-box]]
 
**[[FMN-box]]
 
**[[G-box]]
 
**[[G-box]]
Line 29: Line 32:
 
**[[S-box]]
 
**[[S-box]]
 
**[[Thi-box]]
 
**[[Thi-box]]
 +
**[[YdaO riboswitch]]
 +
**[[YkkC riboswitch]]: ''[[ykkC]]-[[ykkD]], [[yxkD]]''
 +
**[[yybP-ykoY motif]]: ''[[yybP]]'', ''[[ykoY]]''
  
−
* '''Potential additional RNA switches'''
+
* '''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}}  
 
** ''[[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.
 
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=RF00379 ydaO-yuaA switch]: ''[[ydaO]], [[ktrA]]''
 
−
** [http://rfam.sanger.ac.uk/family?acc=RF00442 ykkC-yxkD switch]: ''[[ykkC]], [[yxkD]]''
 
−
** [http://rfam.sanger.ac.uk/family?acc=RF00080 yybP-ykoY switch]: ''[[yybP]]'', ''[[ykoY]]''
 
 
** [http://rfam.sanger.ac.uk/family?acc=RF00516 ylbH switch]: ''[[ylbH]]''
 
** [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=RF00557 L10 leader]: ''[[rplJ]]''
Line 43: Line 47:
 
** L19 leader: ''[[rplS]]''
 
** L19 leader: ''[[rplS]]''
 
** [http://rfam.sanger.ac.uk/family?acc=RF00559 L21_leader]:in front of the ''[[rplU]]-[[ysxB]]-[[rpmA]]'' operon
 
** [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>15063848 , 19385727 19250859 ,19141470 , 17092822, 17764952 ,17381303, 16226486 , 16153177 , 15750802, 14523920  18430893 12029388 19859665 19298181 </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

Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=RNA_switch&oldid=211112"