riboswitch

Summary

Summary: Part of a MESSENGER RNA molecule that undergoes a conformation change upon binding a specific metabolite or other small molecule thereby regulating the messenger RNA's transcription, post-transcriptional processing, transport, translation, or stability in response to varying levels of the metabolite or other small molecule.

Top Publications

  1. Lünse C, Schmidt M, Wittmann V, Mayer G. Carba-sugars activate the glmS-riboswitch of Staphylococcus aureus. ACS Chem Biol. 2011;6:675-8 pubmed publisher
    The glmS-riboswitch is unique among riboswitch families as it represents a metabolite-dependent ribozyme that undergoes self-cleavage upon recognition of glucosamin-6-phosphate...
  2. Manz C, Kobitski A, Samanta A, Keller B, Jäschke A, Nienhaus G. Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch. Nat Chem Biol. 2017;13:1172-1178 pubmed publisher
    ..known about the conformations and motions governing the function of the full-length Bacillus subtilis yitJ SAM-I riboswitch. Therefore, we have explored its conformational energy landscape as a function of Mg2+ and SAM ligand ..
  3. Woods C, Lackey L, Williams B, Dokholyan N, Gotz D, Laederach A. Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo. Biophys J. 2017;113:290-301 pubmed publisher
    ..To validate our approach, we established a conformational map of the Vibrio vulnificus add adenine riboswitch that reveals five classes of structures...
  4. Breaker R, Atilho R, Malkowski S, Nelson J, Sherlock M. The Biology of Free Guanidine As Revealed by Riboswitches. Biochemistry. 2017;56:345-347 pubmed publisher
  5. Sahr T, Rusniok C, Impens F, Oliva G, Sismeiro O, Coppee J, et al. The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system. PLoS Genet. 2017;13:e1006629 pubmed publisher
    ..We describe the first L. pneumophila riboswitch, a thiamine pyrophosphate riboswitch whose regulatory impact is fine-tuned by CsrA, and identified a unique ..
  6. Polaski J, Webster S, Johnson J, Batey R. Cobalamin riboswitches exhibit a broad range of ability to discriminate between methylcobalamin and adenosylcobalamin. J Biol Chem. 2017;292:11650-11658 pubmed publisher
    ..Although this approach has been very successful in identifying new riboswitch families and defining their distributions, small sequence differences between structurally related RNAs can ..
  7. Shiraishi K, Saito Tarashima N, Igata Y, Murakami K, Okamoto Y, Miyake Y, et al. Synthesis and evaluation of c-di-4'-thioAMP as an artificial ligand for c-di-AMP riboswitch. Bioorg Med Chem. 2017;25:3883-3889 pubmed publisher
    Cyclic-di-adenosine monophosphate (c-di-AMP) is a bacterial second messenger that binds to an RNA receptor called riboswitch and regulates its downstream genes involving cell wall metabolism, ion transport, and spore germination...
  8. Chetnani B, MONDRAGON A. Molecular envelope and atomic model of an anti-terminated glyQS T-box regulator in complex with tRNAGly. Nucleic Acids Res. 2017;45:8079-8090 pubmed publisher
    A T-box regulator or riboswitch actively monitors the levels of charged/uncharged tRNA and participates in amino acid homeostasis by regulating genes involved in their utilization or biosynthesis...
  9. Hanke C, Gohlke H. Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch. PLoS ONE. 2017;12:e0179271 pubmed publisher
    ..The guanine-sensing riboswitch (Gsw) binds ligands at a three-way junction formed by paired regions P1, P2, and P3...

More Information

Publications29

  1. Dussault A, Dubé A, Jacques F, Grondin J, Lafontaine D. Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism. RNA. 2017;23:1539-1551 pubmed publisher
    ..Although riboswitch crystal structures provide detailed information about RNA-ligand interactions, little knowledge has been ..
  2. Roy S, Onuchic J, Sanbonmatsu K. Cooperation between Magnesium and Metabolite Controls Collapse of the SAM-I Riboswitch. Biophys J. 2017;113:348-359 pubmed publisher
    The S-adenosylmethionine (SAM)-I riboswitch is a noncoding RNA that regulates the transcription termination process in response to metabolite (SAM) binding...
  3. Mukherjee S, Barash D, Sengupta S. Comparative genomics and phylogenomic analyses of lysine riboswitch distributions in bacteria. PLoS ONE. 2017;12:e0184314 pubmed publisher
    ..hits from multiple strains of the same species) and obtain a detailed phylogenomic map of gene-specific lysine riboswitch distribution across diverse prokaryotic phyla...
  4. di Palma F, Bottaro S, Bussi G. Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations. BMC Bioinformatics. 2015;16 Suppl 9:S6 pubmed publisher
    ..An adenine sensing riboswitch cis-regulates adeninosine deaminase gene (add) in Vibrio vulnificus...
  5. Ferro I, Liebeton K, Ignatova Z. Growth-Rate Dependent Regulation of tRNA Level and Charging in Bacillus licheniformis. J Mol Biol. 2017;429:3102-3112 pubmed publisher
    ..Their tRNA aminoacylation level is kept relatively constant through riboswitch-regulated expression of the cognate aminoacyl-tRNA-synthetase (AARS)...
  6. Garst A, Edwards A, Batey R. Riboswitches: structures and mechanisms. Cold Spring Harb Perspect Biol. 2011;3: pubmed publisher
  7. Zhao B, Guffy S, Williams B, Zhang Q. An excited state underlies gene regulation of a transcriptional riboswitch. Nat Chem Biol. 2017;13:968-974 pubmed publisher
    ..However, we found that the Bacillus cereus fluoride riboswitch aptamer adopts identical tertiary structures in solution with and without ligand...
  8. Rekand I, Brenk R. Ligand design for riboswitches, an emerging target class for novel antibiotics. Future Med Chem. 2017;9:1649-1663 pubmed publisher
    ..In this review, we highlight the most advanced drug design work of riboswitch ligands and discuss the challenges in the field with respect to the development of antibiotics with a new ..
  9. Xiu Y, Jang S, Jones J, Zill N, Linhardt R, Yuan Q, et al. Naringenin-responsive riboswitch-based fluorescent biosensor module for Escherichia coli co-cultures. Biotechnol Bioeng. 2017;114:2235-2244 pubmed publisher
    ..Here we describe the development of an RNA riboswitch-based biosensor module with dual fluorescent reporters, and demonstrate a high-throughput flow cytometry-based ..
  10. Stagno J, Bhandari Y, Conrad C, Liu Y, Wang Y. Real-time crystallographic studies of the adenine riboswitch using an X-ray free-electron laser. FEBS J. 2017;284:3374-3380 pubmed publisher
    Structures of the four reaction states of the adenine riboswitch aptamer domain, including a transient intermediate state were solved by serial femtosecond crystallography...
  11. Batey R. Riboswitches: still a lot of undiscovered country. RNA. 2015;21:560-3 pubmed publisher
  12. Reiss C, Strobel S. Structural basis for ligand binding to the guanidine-II riboswitch. RNA. 2017;23:1338-1343 pubmed publisher
    The guanidine-II riboswitch, also known as mini-ykkC, is a conserved mRNA element with more than 800 examples in bacteria...
  13. Fang X, Michnicka M, Zhang Y, Wang Y, Nikonowicz E. Capture and Release of tRNA by the T-Loop Receptor in the Function of the T-Box Riboswitch. Biochemistry. 2017;56:3549-3558 pubmed publisher
    In Gram-positive bacteria, the tRNA-dependent T-box riboswitch system regulates expression of amino acid biosynthetic and aminoacyl-tRNA synthetase genes through a transcription attenuation mechanism...
  14. Huang L, Wang J, Lilley D. The Structure of the Guanidine-II Riboswitch. Cell Chem Biol. 2017;24:695-702.e2 pubmed publisher
    The guanidine-II (mini-ykkC) riboswitch is the smallest of the guanidine-responsive riboswitches, comprising two stem loops of similar sequence...
  15. Krajewski S, Ignatov D, Johansson J. Two Are Better Than One: Dual Targeting of Riboswitches by Metabolite Analogs. Cell Chem Biol. 2017;24:535-537 pubmed publisher
    ..In methicillin-resistant Staphylococcus aureus (MRSA), ribocil-C and roseoflavin target two autonomous riboswitches simultaneously, thereby inhibiting de novo synthesis and uptake of riboflavin. ..
  16. Bastet L, Chauvier A, Singh N, Lussier A, Lamontagne A, Prévost K, et al. Translational control and Rho-dependent transcription termination are intimately linked in riboswitch regulation. Nucleic Acids Res. 2017;45:7474-7486 pubmed publisher
    ..In the case of the thiamin pyrophosphate-dependent thiM riboswitch, we find that Rho-dependent transcription termination is triggered as a consequence of translation repression...
  17. Wedekind J, Dutta D, Belashov I, Jenkins J. Metalloriboswitches: RNA-based inorganic ion sensors that regulate genes. J Biol Chem. 2017;292:9441-9450 pubmed publisher
    ..This riboswitch-effector interplay produces a layer of gene regulatory feedback that has elicited interest as an antibacterial ..
  18. Wang H, Mann P, Xiao L, Gill C, Galgoci A, Howe J, et al. Dual-Targeting Small-Molecule Inhibitors of the Staphylococcus aureus FMN Riboswitch Disrupt Riboflavin Homeostasis in an Infectious Setting. Cell Chem Biol. 2017;24:576-588.e6 pubmed publisher
    ..As such, riboswitch inhibitors represent a new class of potential antibacterial agents...
  19. Breaker R. Ancient, giant riboswitches at atomic resolution. Nat Struct Mol Biol. 2012;19:1208-9 pubmed publisher
  20. Roth A, Breaker R. Integron attI1 sites, not riboswitches, associate with antibiotic resistance genes. Cell. 2013;153:1417-8 pubmed publisher