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

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)