Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria
- Yale University, United States
- Howard Hughes Medical Institute, United States
Figures
Figure 1
PRPP riboswitches and their regulatory network.
(A) Comparison of the consensus sequence and secondary structure models for the guanidine-I riboswitch aptamer (subtype 1, left) and the aptamers for ppGpp (subtype 2a, middle; ME Sherlock, N …
Figure 2
Ligand binding by a natural singlet PRPP riboswitch.
(A) Sequence and secondary structure of the 106 nucleotide RNA derived from the purC gene of F. ignava. Data collected in B were used to determine regions of constant or reduced scission upon the …
Figure 3 with 1 supplement
Transcription regulation and reporter gene expression by a natural singlet PRPP riboswitch.
(A) Sequence and secondary structure of the natural PRPP singlet riboswitch derived from the purB gene from H. modesticaldum. An alternative RNA structure is depicted in which the terminator stem …
Figure 3—figure supplement 1
Replicate in vitro transcription termination assays with the H.
modesticaldum purB riboswitch construct. Assays are conducted as described for the data generated in Figure 3C. T50 values are estimated to be 40 μM (left) and 80 μM (right).
Figure 4
Ligand binding by tandem guanine and PRPP aptamers.
(A) Sequence and secondary structure of the 208 nucleotide RNA derived from the codA gene of B. megaterium. Data collected in B were used to determine regions of constant, increased, or reduced …
Figure 5 with 1 supplement
Guanine and PRPP competitively regulate transcript termination via a riboswitch integrating two aptamers.
(A) Sequence and secondary structure of the tandem guanine-PRPP riboswitch derived from the codA gene of B. megaterium. An alternative RNA structure is depicted to include the terminator stem …
Figure 5—figure supplement 1
Comprehensive dataset for the in vitro transcription termination assays with the B. megaterium codA riboswitch construct.
Data for three separate transcription termination ‘trials’ are plotted for six conditions tested as noted in panel A. Panels (A) through (F) include the PRPP concentrations used in the assays in the …
Figure 6
Natural examples of tandem riboswitches that approximate Boolean logic functions.
(A) Tandem guanine and PRPP aptamers form an IMPLY logic gate to determine the state of downstream gene expression (express.). (B) Tandem S-adenosylmethionine (SAM) and adenosylcobalamin (AdoCbl) …
Additional files
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Supplementary file 1
This file includes a table listing the DNA constructs used in the study.
- https://doi.org/10.7554/eLife.33908.011
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Supplementary file 2
This file presents a sequence alignment in Stockholm format for individual PRPP riboswitch aptamers.
- https://doi.org/10.7554/eLife.33908.012
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Supplementary file 3
This file presents a sequence alignment in Stockholm format for riboswitches that carry tandem guanine and PRPP aptamers.
- https://doi.org/10.7554/eLife.33908.013
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Transparent reporting form
- https://doi.org/10.7554/eLife.33908.014
