Part:BBa_K2282011

AmilCP with DSbox under Upelmt/CspA promoter + 5'UTR

Usage and Biology

The UP element is believed to stimulate the transcription of the CspA gene at a cold temperature, although some reports conclude the opposite (Phadtare et al., 2005). This promoter plays a role in transcriptional regulation, but not in translation regulation (DSBox, 5’UTR). The CspA promoter is considered a strong promoter (Mitta et al., 1997). The DSbox is a cis-acting mRNA element enabling assembly of the translation pre-initiation complex, likely through interaction with ribosomal protein S1. The 5’ UTR contains a regulatory sequence called “Cold Box”​ that plays an important role in the stabilisation of the mRNA at low temperature (ATTAAA) (Mitta et al, 1997). The structure of this 5’UTR is extremely unstable at high temperature, as it is believed to be hydrolysed by an RNAse, leading to an average lifetime of 12 seconds stability at 37°C, as opposed to 20 minutes at 15°C, a temperature at which the RNAse is no longer active (Barria et al. 2013). All these elements are thought to act synergistically to induce cold-only expression of the amilCP protein.

Source of this part

We used all the sources of our previous parts (BBaK2282006 and BBa_K2282004). Sequences of the 5’UTR, DSBox and other cold-response elements are very close to the parts of the iGEM10_Mexico-UNAM-CINVESTAV that can be found here : http://partsregistry.org/Part:BBa_K328003

Design consideration

This part sums up our final cold regulated construction. A lot of planning was done to develop our strategy and sequences. The overall strategy we chose is complex and we were not sure if it would work. Through bibliographic study of open source literature, the iGEM Parts Registry, and industrial patents, we saw that the iGEM10_Mexico-UNAM-CINVESTAV team attempted the same strategy as us, but nothing was said on their wiki regarding their results. We also saw that the pCOLD vector from the company Takara also used the same technology, with some variations, and was patented. We therefore thought that this strategy had a good chance of success.

Below is presented the 3D structure of the cspA 5'UTR as computed by SimRNA (a coarse grained statistical potential method for RNA folding simulations). Highlighted in yellow is the DS box sequence, which is important for increased expression levels at low temperatures, and forms part of the coding sequence.

Characterisation

Pre-incubation of transformed bacteria were set up at 37°C until the O.D. reached 0.5. Then they were cultured at different temperatures (12°C, 15°C, 20°C) with a control at 37°C

After centrifuging bacteria, the pellet of bacteria transformed with BBa K2282011 appeared blue at 15°C but not at 37°C. These results were in accordance with the hypothesis. We tried 18h incubation and 42h to see any change in intensity but it seemed that there was no difference. Therefore, further experiments were only carried out during 20h.

The experiment was also carried out at 18°C and 12°C in an attempt to determine a shift.

At 20°C after 20°C, bacteria transformed with BBa K2282011 were also blue compared to the wild type bacteria.

Same results at 12°C.

The shift should therefore occur between 20°C and 37°C. Plus, the regulatory machine is active until at least 12°C.

References

Phadtare S, Severinov K. Extended −10 Motif Is Critical for Activity of the cspA Promoter but Does Not Contribute to Low-Temperature Transcription. Journal of Bacteriology. 2005;187(18):6584-6589. doi:10.1128/JB.187.18.6584-6589.2005.

Masanori Mitta et al, Deletion analysis of cspA of Escherichia coli requirement of the AT-rich UP element for cspA transcription and the downstream box in the coding region for its cold shock induction, Molecular Microbiology (1997) 26(2), 321–335

C. Barria et al, “Bacterial adaptation to cold”, Microbiology (2013), 159, 2437–2443

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  INCOMPATIBLE WITH RFC[21]

  Unknown
• 23
  COMPATIBLE WITH RFC[23]
• 25
  COMPATIBLE WITH RFC[25]
• 1000
  COMPATIBLE WITH RFC[1000]