sRNATarBase (original) (raw)

sRNA Target

[Next]

| Reference 1 | | | | | | ----------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | ----- | -------------------------------------------------------------------- | | Title | Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci. | | | | | Author | Lease RA, Cusick ME, Belfort M. | | | | | Citation | Proc Natl Acad Sci U S A. 1998, 95(21):12456-61. | | | | | PMID | 9770507 | | | | | Direct Support | Point mutation of sRNA | | | | | Indirect Support | Primer extension;Western blot;Overexpression;IFE(isoelectric focusing electrophoresis) | | | | | Hfq Need | no | | | | | sRNA Binding Position | 31..43 [Predicted Structure] | | | | | Target Binding Position | 7..19 [Predicted Structure] | | | | | Interaction | Target 5'-gaagcacttaaaa-3' ||||||||||||| sRNA 3'-cttcgtgaatttt-5' | | | | | Mutation | No. Type Name Position Original Sequence Mutation Sequence 1 mRNA M1 9 A G [Predicted Structure][Predicted Structure] 2 mRNA M2 12..13 AC CT [Predicted Structure][Predicted Structure] 3 mRNA M3 15 T G [Predicted Structure][Predicted Structure] 4 mRNA M4 18 A G [Predicted Structure][Predicted Structure] 5 sRNA M1 12..14 TTT CCC [Predicted Structure][Predicted Structure] 6 sRNA M2 24..25 AC CA [Predicted Structure][Predicted Structure] 7 sRNA M3 29..30 TT AG [Predicted Structure][Predicted Structure] | | | | | Description | DsrA acts via specific RNA:RNA base pairing interactions at the hns locus to antagonize H-NS translation. We also give evidence that supports a role for RNA:RNA interactions at the rpoS locus to enhance RpoS translation. Negative regulation of hns by DsrA is achieved by the RNA:RNA interaction blocking translation of hns RNA. In contrast, results suggest that positive regulation of rpoS by DsrA occurs by formation of an RNA structure that activates a cis-acting translational operator. | | | | | Reference 2 | | | | | | Title | Translational control and target recognition by Escherichia coli small RNAs in vivo. | | | | | Author | Urban JH, Vogel J. | | | | | Citation | Nucleic Acids Research. 2007, 35(3):1018-37. | | | | | PMID | 17264113 | | | | | Direct Support | mRNA Reporter gene assay(mRNA::GFP fusion) | | | | | Indirect Support | 5'RACE;Northern blot;Western blot | | | | | Hfq Need | yes | | | | | sRNA Binding Position | N_A | | | | | Target Binding Position | N_A | | | | | Interaction | N_A | | | | | Description | DsrA represses hns mRNA by binding it at both the start and the stop codon region; in other words,a bipartite interaction that would involve regions within the hns mRNA that are 400 nt apart.Most of these sRNA plasmids had a negligible effect on GFP fluorescence, whereas DsrA,RyhB and Spot42 positively changed fluorescence up to 1.5-fold. | | | | | Reference 3 | | | | | | Title | A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures. | | | | | Author | Lease RA, Belfort M. | | | | | Citation | Proc Natl Acad Sci U S A. 2000, 97(18):9919-24. | | | | | PMID | 10954740 | | | | | Direct Support | Footprinting analysis | | | | | Indirect Support | 5'RACE; Northern blot; Western blot; Nuclease Cleavage Assays | | | | | Hfq Need | N_A | | | | | sRNA Binding Position | 31..54 [Predicted Structure] | | | | | Target Binding Position | 7..19,401..411 [Predicted Structure] | | | | | Interaction | Target 5'-tgatcaagcaa-taa-3' 5'-atgagcgaagcacttaaaa-3' || | | ||||| | |||||||||||| sRNA 3'-acgaattcgtt-...............-cttcgtgaatttt-5' | | Description | The DsrA-complementary region within hns described was initially found by computer alignment and verified by compensatory mutagenesis. A computational reexamination of the hns coding sequence revealed a second potential interaction of hns with DsrA. Interestingly, whereas the previously described complementary sequence is near the start codon for hns translation, the second region is near the hns stop codon. Base pairing between DsrA and the two regions of hns would form a contiguous coaxial stack, looping out the middle part of hns mRNA. | | | |