Team:Stuttgart/Part Collection
Parts
Part Collection
V. natriegens rare tRNA collection
We present the V.natriegens rare tRNA collection from Team Stuttgart. The collection contains the 5 rarest tRNA genes from the genome of Vibrio natriegens. Applying the High-performance Integrated Virtual Environment-Codon Usage Tables (HIVE-CUTs) databank codon usage tables were generated for Vibrio natriegens (DSM759) using the online interface (available at hive.biochemistry.gwu.edu/review/codon).1 From this codon usage tables codons were selected as a 'rare' codon, if the number of codons per 1000 codons was less or equal 5 (excluding the stop-codons ‘TAA’, ‘TAG’ and ‘TGA’).The encoded tRNA genes were identified using tRNA-Scan. 2 For all rare tRNAs, except the CCC(Proline)-encoding tRNA, genes were successfully identified. The parts have been synthesized by Integrated DNA Technologies with Biobrick cloning sites to ensure easy cloning through the BioBrick Standard Assembly.
The system is based on the famous Rosetta strain with pRARE from Merck.3 pRARE contains the rarest codons of E. coli to increase the translation rate. We are pursuing a similar system with the V. natriegens rare tRNA collection. However, all iGEM teams have access to this system and can fully exploit the potential of V. natriegens. In this way, we contribute towards optimizing V. natriegens with the aim of replacing E. coli as the most commonly used organism in the future.
| Pos | Name | Type | Description | Designer | Length |
|---|---|---|---|---|---|
| Pos | Name | Type | Description | Designer | Length |
| 1 | BBa_K3014000 | Coding | Vibrio natriegens tRNA AGA | Benedikt Schober, Jan Müller, Kai Schülke | 135 |
| 2 | BBa_K3014001 | Coding | Vibrio natriegens tRNA AGG | Benedikt Schober, Jan Müller, Kai Schülke | 135 |
| 3 | BBa_K3014002 | Coding | Vibrio natriegens tRNA CGG | Benedikt Schober, Jan Müller, Kai Schülke | 160 |
| 4 | BBa_K3014003 | Coding | Vibrio natriegens tRNA TGC | Benedikt Schober, Jan Müller, Kai Schülke | 161 |
| 5 | BBa_K3014004 | Coding | Vibrio natriegens tRNA TCC | Benedikt Schober, Jan Müller, Kai Schülke | 151 |
| 6 | BBa_K3014012 | Coding | Vibrio natriegens tRNA construct | Benedikt Schober, Jan Müller, Kai Schülke | 915 |
References
- Athey J, Alexaki A, Osipova E, Rostovtsev A, Santana-quintero L V. A new and updated resource for codon usage tables. 2017:1-10. doi:10.1186/s12859-017-1793-7.
- Lowe TM, Chan PP. tRNAscan-SE On-line : integrating search and context for analysis of transfer RNA genes. 2016;44(May):54-57. doi:10.1093/nar/gkw413
- Robert Novy, Don Drott KY and RM. Overcoming the codon bias of E. coli for enhanced protein expression. Newsl NOVAGEN, INC. 2001;(12):4-6.