Difference between revisions of "Part:BBa K5097001"
Elberlopezh (Talk | contribs) |
Elberlopezh (Talk | contribs) |
||
| (One intermediate revision by the same user not shown) | |||
| Line 7: | Line 7: | ||
Pham et. al. reported that the putative RBS within the PRE riboswitch is of weak affinity. These researchers designed an improved version, PREmR34, which contains the strong RBS (Bba_B0034) (3). We utilized RNAfold (4) to model the structure of the PREm34, which is, expected, very similar to that of PRE. We also performed a Pairwise alignment on the sequences to visualize change. | Pham et. al. reported that the putative RBS within the PRE riboswitch is of weak affinity. These researchers designed an improved version, PREmR34, which contains the strong RBS (Bba_B0034) (3). We utilized RNAfold (4) to model the structure of the PREm34, which is, expected, very similar to that of PRE. We also performed a Pairwise alignment on the sequences to visualize change. | ||
| − | + | :::https://static.igem.wiki/teams/5097/parts/team-oneonta-2024-pre-m34model0.jpg | |
| − | + | ::Figure 1: Structure of PRE and PREmR34 riboswitches. The sequences of these two iterations of the PRE riboswitch were modeled in RNAFold, and the Forna structures were visualized (4,5). No significant differences in the structure of the riboswitch are apparent, save for a longer stem structure in PREmR34, created by the replacement of the native RBS with B0034, and the modification of the complementary region at the beginning of the riboswitch. | |
| − | + | :::https://static.igem.wiki/teams/5097/parts/team-oneonta-2024-pre-m34-alignment00.jpg | |
| − | + | ::Figure 2: Pairwise alignment of the PRE riboswitch (Bba_K5097000) and PREmR34 (this part) illustrating the changes introduced to replace the native RBS. | |
===References=== | ===References=== | ||
| − | 1. Bingham, R J, et al. “Alkaline Induction of a Novel Gene Locus, ALX, in Escherichia Coli.” Journal of Bacteriology, U.S. | + | 1. Bingham, R J, et al. “Alkaline Induction of a Novel Gene Locus, ALX, in Escherichia Coli.” Journal of Bacteriology, U.S. |
| + | |||
| + | 2. National Library of Medicine, Apr. 1990, www.ncbi.nlm.nih.gov/pmc/articles/PMC208722/. | ||
| + | |||
3. Nechooshtan, Gal, et al. “A PH-Responsive Riboregulator.” Genes & Development, U.S. National Library of Medicine, 15 Nov. 2009, www.ncbi.nlm.nih.gov/pubmed/19933154. | 3. Nechooshtan, Gal, et al. “A PH-Responsive Riboregulator.” Genes & Development, U.S. National Library of Medicine, 15 Nov. 2009, www.ncbi.nlm.nih.gov/pubmed/19933154. | ||
| + | |||
4. Pham, H., Wong, A., Chua, N. et al. Engineering a riboswitch-based genetic platform for the self-directed evolution of acid-tolerant phenotypes. Nat Commun 8, 411 (2017). https://doi.org/10.1038/s41467-017-00511-w | 4. Pham, H., Wong, A., Chua, N. et al. Engineering a riboswitch-based genetic platform for the self-directed evolution of acid-tolerant phenotypes. Nat Commun 8, 411 (2017). https://doi.org/10.1038/s41467-017-00511-w | ||
| + | |||
5. Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL. The Vienna RNA Websuite. Nucleic Acids Research, Volume 36, Issue suppl_2, 1 July 2008, Pages W70-W74, DOI: 10.1093/nar/gkn188 | 5. Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL. The Vienna RNA Websuite. Nucleic Acids Research, Volume 36, Issue suppl_2, 1 July 2008, Pages W70-W74, DOI: 10.1093/nar/gkn188 | ||
https://www.genome.jp/tools-bin/clustalw | https://www.genome.jp/tools-bin/clustalw | ||
Latest revision as of 21:08, 30 September 2024
pH Response Element riboswitch mR34
In 1990, Bingham et al. identified a locus within E.coli whose activity was tied to pH changes, which they coined Alx. It exhibited increased expression at pH 8.5 (1). This activity was further characterized by Nechooshtan et. al., who determined that the Alx promoter and riboswitch are responsible for increased Alx expression in response to high pH (2). The Alx promoter and riboswitch have been previously entered into the parts repository by Team NAXI_GRAS under part number BBa_K2348000.
Pham et. al. reported that the putative RBS within the PRE riboswitch is of weak affinity. These researchers designed an improved version, PREmR34, which contains the strong RBS (Bba_B0034) (3). We utilized RNAfold (4) to model the structure of the PREm34, which is, expected, very similar to that of PRE. We also performed a Pairwise alignment on the sequences to visualize change.
- Figure 1: Structure of PRE and PREmR34 riboswitches. The sequences of these two iterations of the PRE riboswitch were modeled in RNAFold, and the Forna structures were visualized (4,5). No significant differences in the structure of the riboswitch are apparent, save for a longer stem structure in PREmR34, created by the replacement of the native RBS with B0034, and the modification of the complementary region at the beginning of the riboswitch.
- Figure 2: Pairwise alignment of the PRE riboswitch (Bba_K5097000) and PREmR34 (this part) illustrating the changes introduced to replace the native RBS.
References
1. Bingham, R J, et al. “Alkaline Induction of a Novel Gene Locus, ALX, in Escherichia Coli.” Journal of Bacteriology, U.S.
2. National Library of Medicine, Apr. 1990, www.ncbi.nlm.nih.gov/pmc/articles/PMC208722/.
3. Nechooshtan, Gal, et al. “A PH-Responsive Riboregulator.” Genes & Development, U.S. National Library of Medicine, 15 Nov. 2009, www.ncbi.nlm.nih.gov/pubmed/19933154.
4. Pham, H., Wong, A., Chua, N. et al. Engineering a riboswitch-based genetic platform for the self-directed evolution of acid-tolerant phenotypes. Nat Commun 8, 411 (2017). https://doi.org/10.1038/s41467-017-00511-w
5. Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL. The Vienna RNA Websuite. Nucleic Acids Research, Volume 36, Issue suppl_2, 1 July 2008, Pages W70-W74, DOI: 10.1093/nar/gkn188 https://www.genome.jp/tools-bin/clustalw
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000INCOMPATIBLE WITH RFC[1000]Illegal BsaI.rc site found at 126