The cotranscriptional folding landscape for two cyclic di-nucleotide-sensing riboswitches with highly homologous aptamer domains acting either as ON- or OFF-switches
- Riboswitches are gene regulatory elements located in untranslated mRNA regions. They bind inducer molecules with high affinity and specificity. Cyclic-di-nucleotide-sensing riboswitches are major regulators of genes for the environment, membranes and motility (GEMM) of bacteria. Up to now, structural probing assays or crystal structures have provided insight into the interaction between cyclic-di-nucleotides and their corresponding riboswitches. ITC analysis, NMR analysis and computational modeling allowed us to gain a detailed understanding of the gene regulation mechanisms for the Cd1 (Clostridium difficile) and for the pilM (Geobacter metallireducens) riboswitches and their respective di-nucleotides c-di-GMP and c-GAMP. Binding capability showed a 25 nucleotide (nt) long window for pilM and a 61 nt window for Cd1. Within this window, binding affinities ranged from 35 μM to 0.25 μM spanning two orders of magnitude for Cd1 and pilM showing a strong dependence on competing riboswitch folds. Experimental results were incorporated into a Markov simulation to further our understanding of the transcriptional folding pathways of riboswitches. Our model showed the ability to predict riboswitch gene regulation and its dependence on transcription speed, pausing and ligand concentration.
Author: | Tom LandgrafORCiDGND, Albrecht Eduard VölkleinORCiDGND, Boris FürtigORCiDGND, Harald SchwalbeORCiDGND |
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URN: | urn:nbn:de:hebis:30:3-633131 |
DOI: | https://doi.org/10.1093/nar/gkac514 |
ISSN: | 1362-4962 |
Parent Title (English): | Nucleic acids research |
Publisher: | Oxford Univ. Press |
Place of publication: | Oxford |
Document Type: | Article |
Language: | English |
Date of Publication (online): | 2022/06/23 |
Date of first Publication: | 2022/06/23 |
Publishing Institution: | Universitätsbibliothek Johann Christian Senckenberg |
Release Date: | 2023/04/04 |
Volume: | 50 |
Issue: | 12 |
Page Number: | 17 |
First Page: | 6639 |
Last Page: | 6655 |
Note: | Funding: DFG priority program [SPP 1879]; collaborative research center [SFB902]; work at BMRZ is supported by the state of Hesse. Funding for open access charge: institutional funds. |
Note: | DATA AVAILABILITY mFold: http://unafold.rna.albany.edu/?q = mfold Sedphat: http://www.analyticalultracentrifugation.com/sedphat/download.htm NITPIC: http://biophysics.swmed.edu/MBR/software.html Sparky: https://www.cgl.ucsf.edu/home/sparky/ Topspin: https://www.bruker.com/service/support-upgrades/software-downloads/nmr/free-topspin-processing/nmr-topspin-license-for-academia.html. |
HeBIS-PPN: | 508949106 |
Institutes: | Biochemie, Chemie und Pharmazie |
Dewey Decimal Classification: | 5 Naturwissenschaften und Mathematik / 54 Chemie / 540 Chemie und zugeordnete Wissenschaften |
Sammlungen: | Universitätspublikationen |
Licence (German): | Creative Commons - CC BY - Namensnennung 4.0 International |