IGEM:IMPERIAL/2008/Sequence: Difference between revisions
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More improtantly, the ''B.subtilis'' RBS appears to be a 9bp sequence complementary to the a section of the 16S rRNA (3' end) from the 30S ribosome small subunit.<cite>#11</cite> It is indicated that this may be due to a lack of the S1 protein in the ''B.subtilis'' ribosome.<cite>#12</cite>. The complementary sequence is 5'-AAGGAGGTG-3' | |||
As such, any sequence with high homology to this sequence may be used, in particular,Thorsted et al. (1999)<cite>#13</cite> identified several putative RBSs in a ''B.subtilis'' vector that have reasonable homology. It may also be possible to simply use the complementary sequence to use as our RBS. | |||
#11 pmid=9678589 | |||
#12 pmid=3937526 | |||
#13 pmid=10366533 | |||
===The Parts Grave Yard=== | ===The Parts Grave Yard=== | ||
Revision as of 05:28, 30 July 2008
Hello Team Sequence, Thought we could use this page to load up all the information. If we could load up the sequence of the parts here, probably load the pure sequence then one with the restriction sites on the end. Here are some useful websites about the ends:
- http://partsregistry.org/Help:BioBrick_Prefix_and_Suffix
- http://partsregistry.org/Assembly:RBS-CDS_issues
To do list
- Tom - Find transcription terminators for B.subtilis, Two papers to start with are here
- Finish triple check
- Chris - How were the RBS derived? - By locating the sequence between gene and promoter on NCBI sequence viewer
- Get sequence for LacI -> Registry part found: BBa_C0012 [1]
- Get sequence for xylR if needed Sequence found
- Choose parts we want to use
- Work out assembly
Parts
First thing tomorrow we need to get a group together (preferably with Kirsten) and decide about whether to use stand-alone RBSs or use Promoter-RBS or RBS-gene combinations
- Just had a thought, can we reuse lacI from the registry, ill check operon binding sites but if its a hybrid i guess its the same
- Sequence is the same as the Biobrick version
- RBS- the alternate paper I included has three potential RBS with the sequence included. These are gsiA,gsiB and ctc. Thinking gsiB and ctc would be good one as the paper calculated the expected binding efficiencies and these two give us a good range.
| Part Class | Part Name | Sequence File | Papers/References | Checked | Biobrick Length (bp) |
| Promoter | |||||
| 1.Promoter - Light | Pctc | Pctc Biobrick |
Paper DBTBS | J, QQ, C | 99bp |
| 2.Promoter - σB | PgsiB | PgsiB Biobrick |
Paper DBTBS | J, C, QQ | 81bp |
| 3.Promoter - ComK upregulated | PcomC | PcomC Biobrick |
DBTBS Paper | C, J, QQ | 137bp |
| 4.Promoter - Constitutuive | P43 | P43 Biobrick |
Paper Paper2 |
C, J, QQ | 99bp |
| 5.Promoter - Inducible | Phyper-spank | Ph-s Biobrick |
Dr. Angelika Grundling (Imperial College London), Dr. Jan-Willem Veening (Newcastle University), Paper1, Paper2, Paper3, NEBcutter2 | C, J | 145bp |
| 6.Promoter - Inducible | Pxyl | Pxyl Biobrick |
Dr. Jan-Willem Veening (Newcastle University), DBTBS, Paper1, Paper2 | C - has been fixed | 125bp |
| 7.Promoter - Contitutive (high) | Pveg | Pveg Biobrick |
Dr. Jan-Willem Veening (Newcastle University), DBTBS | C, J, QQ | 87 |
| RBS | |||||
| 1.RBS - Stong | RBS-gsiB | Alt RBS Biobrick | Alt paper reference | J | 57 |
| 2.RBS - Strong | RBS-ctc | Biobrick | Alt paper reference | J | 51 |
| Gene | |||||
| 1.Gene | epsE | Protein Biobrick |
Page 9, Online Supplementary Material for "A Molecular Clutch Disables Flagella in the Bacillus subtilis Biofilm" | QQ, J | 878 |
| 2.Gene | ytvA | Protein Biobrick |
Partial sequence (LOV domain) | QQ, J | 786 |
| 3.Gene | sinR | Protein Biobrick |
- | QQ, J | 377 |
| 4.Biomaterial | EP24-20-20 | Biobrick | Paper | QQ, J | 640 |
| 5.Biomaterial | EAK16-II | Biobrick | Paper | QQ, J | 92 |
| 6.Signal Peptide | SacB | Biobrick | Paper for signal peptide | QQ, J | 139 |
| 7.Signal Peptide | LipA | Biobrick | Paper for signal peptide | 145 | |
| 8.Signal Peptide | Epr | Biobrick | Paper for signal peptide | 133 | |
| Terminator |
More improtantly, the B.subtilis RBS appears to be a 9bp sequence complementary to the a section of the 16S rRNA (3' end) from the 30S ribosome small subunit.[1] It is indicated that this may be due to a lack of the S1 protein in the B.subtilis ribosome.[2]. The complementary sequence is 5'-AAGGAGGTG-3'
As such, any sequence with high homology to this sequence may be used, in particular,Thorsted et al. (1999)[3] identified several putative RBSs in a B.subtilis vector that have reasonable homology. It may also be possible to simply use the complementary sequence to use as our RBS.
- 11 pmid=9678589
- 12 pmid=3937526
- 13 pmid=10366533
The Parts Grave Yard
For those parts that never made, rest in peace!!
| Part Class | Part Name | Sequence File | Papers/References | Checked | Biobrick Length (bp) |
| Terminator | |||||
| 1.Terminator | TermI-VI Consensus of 6 terminators |
6NSCT Protein Biobrick |
Search for additional replication terminators in the Bacillus subtilis chromosome | For rep not scrip - BRB, killing self ~ Tom Adie 09:41, 30 July 2008 (UTC) | 30bp |
| 2.Terminator | rrnO | rrnO Biobrick | Dr. Jan-Willem Veening (Newcastle University) | 133bp (with extra frame-shift base) | |
| 3.Terminator | rrnA | rrnA Biobrick | Dr. Jan-Willem Veening (Newcastle University) | 132bp (with extra frame-shift base) | |
| RBS | |||||
| 2.RBS - Strong | RBS-spoVG | RBS-spoVG Biobrick |
Paper (reference only) DBTBS | C, Sorry not sure how this one was worked out | 68bp |
| 3.RBS - Strong | RBS-PBS | RBS-PBS Biobrick |
Dr. Jan-Willem Veening (Newcastle University), Paper | Issues - C | |
| 4.RBS - Strong | RBS-ctc | Biobrick | Alt paper reference | J | 57 |
