RNA switch

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

• Protein-dependent RNA switches
  • 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 TRAP
  • hutH-hutU-hutI-hutG-hutM: controlled by HutP
  • pyrR-pyrP-pyrB-pyrC-pyrAA-pyrAB-pyrK-pyrD-pyrF-pyrE: controlled by PyrR

• tRNA-dependent RNA switches: T-box

• Metabolite-dependent RNA switches: Riboswitches
  • A-box
  • FMN-box
  • G-box
  • Gly-box
  • L-box
  • M-box
  • preQ1 riboswitch
  • ribozyme: glmS
  • S-box
  • Thi-box
  • YdaO riboswitch

• 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.

• • yjdF switch: yjdF PubMed
  • ykkC-yxkD switch: ykkC, yxkD
  • yybP-ykoY switch: yybP, ykoY
  • ylbH switch: ylbH
  • L10 leader: rplJ
  • L13 leader: rplM
  • L19 leader: rplS
  • L21_leader:in front of the rplU-ysxB-rpmA operon

• RNA switch candidates PubMed, 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

Important Reviews

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] (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] (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)