Skip to main content
Article thumbnail
Location of Repository

Design Principles for Riboswitch Function

By Chase L. Beisel and Christina D. Smolke


Scientific and technological advances that enable the tuning of integrated regulatory components to match network and system requirements are critical to reliably control the function of biological systems. RNA provides a promising building block for the construction of tunable regulatory components based on its rich regulatory capacity and our current understanding of the sequence–function relationship. One prominent example of RNA-based regulatory components is riboswitches, genetic elements that mediate ligand control of gene expression through diverse regulatory mechanisms. While characterization of natural and synthetic riboswitches has revealed that riboswitch function can be modulated through sequence alteration, no quantitative frameworks exist to investigate or guide riboswitch tuning. Here, we combined mathematical modeling and experimental approaches to investigate the relationship between riboswitch function and performance. Model results demonstrated that the competition between reversible and irreversible rate constants dictates performance for different regulatory mechanisms. We also found that practical system restrictions, such as an upper limit on ligand concentration, can significantly alter the requirements for riboswitch performance, necessitating alternative tuning strategies. Previous experimental data for natural and synthetic riboswitches as well as experiments conducted in this work support model predictions. From our results, we developed a set of general design principles for synthetic riboswitches. Our results also provide a foundation from which to investigate how natural riboswitches are tuned to meet systems-level regulatory demands

Topics: Research Article
Publisher: Public Library of Science
OAI identifier:
Provided by: PubMed Central

Suggested articles


  1. (2007). A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function.
  2. (2007). A modular and extensible RNA-based generegulatory platform for engineering cellular function.
  3. (2000). A singlemolecule study of RNA catalysis and folding.
  4. (2005). An obligate intermediate along the slow folding pathway of a group II intron ribozyme.
  5. (2006). Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction.
  6. (1999). Attenuation of green fluorescent protein half-life in mammalian cells.
  7. (2006). Codeine-binding RNA aptamers and rapid determination of their binding constants using a direct coupling surface plasmon resonance assay.
  8. (2008). Complex riboswitches.
  9. (2003). Conditional gene expression by controlling translation with tetracycline-binding aptamers.
  10. (2007). Control of alternative RNA splicing and gene expression by eukaryotic riboswitches.
  11. (2004). Control of gene expression by a natural metabolite-responsive ribozyme.
  12. (1995). Control of the Escherichia coli rrnB P1 promoter strength by ppGpp.
  13. (2006). Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid.
  14. (2008). Direct observation of hierarchical folding in single riboswitch aptamers.
  15. (2002). Directed evolution of a genetic circuit. Proc Natl Acad Sci
  16. (2004). Engineered riboregulators enable post-transcriptional control of gene expression.
  17. (2008). Engineered riboswitches: Overview, problems and trends.
  18. (2006). Folding of the adenine riboswitch.
  19. (2004). Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation.
  20. (2007). Genomewide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana.
  21. (2002). Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays.
  22. (2003). Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation.
  23. (2007). Guiding bacteria with small molecules and RNA.
  24. (1994). High-resolution molecular discrimination by RNA.
  25. (2000). HIV-1 reverse transcriptase-pseudoknot RNA aptamer interaction has a binding affinity in the low picomolar range coupled with high specificity.
  26. (2008). How RNA unfolds and refolds.
  27. (2004). Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.
  28. (2004). Just-intime transcription program in metabolic pathways.
  29. (2007). Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control.
  30. (2007). Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach.
  31. (2007). Measuring the folding transition time of single RNA molecules.
  32. (2007). Mechanism of mRNA destabilization by the glmS ribozyme.
  33. (2008). Metabolic gene regulation in a dynamically changing environment.
  34. (2008). Model-guided design of ligand-regulated RNAi for programmable control of gene expression.
  35. (2008). Natural variability in Sadenosylmethionine (SAM)-dependent riboswitches: S-box elements in bacillus subtilis exhibit differential sensitivity to SAM In vivo and in vitro.
  36. (1997). Nucleic acid selection and the challenge of combinatorial chemistry.
  37. (2005). Optimality and evolutionary tuning of the expression level of a protein.
  38. (2008). Oudenaarden A
  39. (2000). Pardi A
  40. (2006). Quantification of protein half-lives in the budding yeast proteome.
  41. (2008). Random walks to synthetic riboswitches—a highthroughput selection based on cell motility.
  42. (2002). Real-time RT-PCR analysis of mRNA decay: half-life of Beta-actin mRNA
  43. (2005). Riboswitches and the role of noncoding RNAs in bacterial metabolic control.
  44. (2003). Ribozyme speed limits.
  45. (2008). RNA dynamics: it is about time.
  46. (2006). RNA folding during transcription.
  47. (2006). RNA synthetic biology.
  48. (2006). RNAKinetics: a web server that models secondary structure kinetics of an elongating RNA.
  49. (2000). Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties.
  50. (1996). Slow folding kinetics of RNase P RNA.
  51. Smolke CD (2005) Programmable ligand-controlled riboregulators of eukaryotic gene expression.
  52. (2006). Structural basis of glmS ribozyme activation by glucosamine-6-phosphate.
  53. (2005). The Bacillus subtilis sin operon: an evolvable network motif.
  54. (2007). The distributions, mechanisms, and structures of metabolite-binding riboswitches.
  55. (2005). The kinetics of ligand binding by an adenine-sensing riboswitch.
  56. (2008). The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data.
  57. (1974). The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA.
  58. (2005). The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch.
  59. (2007). Tunability and noise dependence in differentiation dynamics.

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.