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
  • B12 riboswitch
  • FMN-box
  • G-box
  • Gly-box
  • L-box
  • M-box
  • preQ1 riboswitch
  • ribozyme: glmS
  • 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
  • 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
  • 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 Original Publications

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

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)