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Part:BBa_B0034:Experience
This experience page is provided so that any user may enter their experience using this part.
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how you used this part and how it worked out.
Applications of BBa_B0034
User Reviews
UNIQ3069885b64ce3b31-partinfo-00000000-QINU
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Antiquity |
This review comes from the old result system and indicates that this part worked in some test. |
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Aberdeen_Scotland 2009 |
Our miniprep, double digest and gel worked properly. We used this part in fusion PCR for building our biobrick BBa_K182102. The fusion PCR, cloning and sequence were all correct. |
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iGEM Groningen 2009 |
The ligation of part BBa_K190028 behind the RBS was successful, confirmed by gel (correct vector size after digestion with EcoRI and PstI) and sequencing with VF2 primer. We used this part in combination with several genes for building our biobricks e.g. BBa_K190061. |
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maven |
Defining efficiency for an RBS seems misleading, since RBS efficiency can only be considered in context of its upstream and downstream sequences as this [http://www.nature.com/nbt/journal/v27/n10/abs/nbt.1568.html article] demonstrated. |
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iGEM Copenhagen |
We attempted to use this BioBrick to assembly a protein expressing device. We were unable to do it with standard assembly but had succesful result utilizing the 2011 [http://2011.igem.org/Team:Copenhagen/Collaboration| DTU-2 user assembly plug'n'play method] |
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iGEM Amsterdam 2011 |
Our results show proteins can be expressed at low temperatures using this RBS. From this we conclude that the RBS is useful for translation in cold environments. |
UNIQ3069885b64ce3b31-partinfo-0000000A-QINU
UNIQ3069885b64ce3b31-partinfo-0000000B-QINU
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UNIPV-Pavia iGEM 2011 |
NB: unless differently specified, all tests were performed in E. coli MGZ1 in M9 supplemented medium at 37°C in low copy plasmid pSB4C5.
The complex RBS-promoter acts as a whole regulatory element and determines the amount of translated protein. RBSs have been reported to have an un-modular behavior, since the translational efficiency is not independent on the coding sequences, but variates as an effect of different mRNA structure stability [Salis et al., Nat Biotec, 2009]. In addition, it is not possible to separate the effects of the sole promoter and of the sole RBS on the total amount of protein produced.
For this reason, every combination 'Promoter+RBS' was studied as a different regulatory element.
The evaluation of RBS efficiency can be performed in a very intuitive fashion:
This simple measurement system allows the quantification of RBS efficiency depending on the experimental context (i.e.: promoter and encoded gene). Today it has not still been completely validated the hypothesis that every functional module in a genetic circuit maintains its behavior when assembled in complex circuits, even if many researchers implicitly accept this hypothesis when performing characterization experiments. To rationally assess the impact that this hypothesis has on the genetic circuit design and fine tuning, several measurement systems were built to evaluate the dependance of RBS modularity from the promoter or the coding sequence separately. In particular, in order to investigate if RBS efficiency depends on the promoter, the same coding devices (RBSx-RFP-TT) were assembled downstream of different promoters (J23101, pTet, pLux). The system output was measured and the RBS efficiency evaluated. The results are summarized in the table below:
On the other hand, to investigate the dependance of RBS modularity on the coding sequence, the same regulatory elements (pTet-RBSx) were assembled upstream of different encoded gene (mRFP, AiiA and LuxI). RBS efficiency was assessed and the results are summarized in the table below:
* The RBS efficiency for inducible devices expressing mRFP was estimated as the ratio of the AUCs (Area under the curve) of the induction curve of the system with the studied RBS and the B0034 reference: AUCP, RBSx/AUCP, B0034 ** The RBS efficiency for constitutive promoters expressing mRFP was computed as the ratio between ScellP, RBSx/ScellP, B0034 *** The RBS efficiency for pTet promoter driving the expression of AiiA enzyme was computed as the ratio between the percentage of degraded HSL after 7 hours of the studied system and the reference B0034 in E. coli TOP010, in high copy number plasmid pSB1A2. **** The RBS efficiency for promoters driving the expression of LuxI was computed as the ratio αpTet, RBSx/αpTet, B0034 estimated from the measurement systems pTet-RBSx-LuxI. αpTet was estimated as described here. pTet was tested at full induction (100 ng/ml). The parts we used to characterize the RBSs are listed here:
The results reported in the table suggest that the RBS efficiency ranking is not always maintained. In particular, for the different promoters driving the expression of mRFP, the ranking of the declared efficiencies is maintained for pLux, but not for pTet and J23101. The RBS B0030 results to be the most efficient for both J23101 and pTet, but not for pLux (NB: this effect might be due to an effective non-modularity of RBS, but also to saturating phenomena occurring for this very strong promoter at full induction). RBS B0031 always shows a very low efficiency, while B0032 an intermediate efficiency between B0031 and the stronger RBSs B0030 and B0034. These results are encouraging: though the partial non-modularity of RBS with the encoded gene is confirmed, the hypothesis of modularity with the promoter is to some extent confirmed. Three classes of efficiencies were identified:
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UNIQ3069885b64ce3b31-partinfo-0000000E-QINU