Difference between revisions of "Part:BBa K2282009"

Revision as of 12:15, 25 October 2017

Usage and biology

This sequence is used to evaluate our cold shock response. The UP element is believed to stimulate the transcription of the CspA gene at a cold temperature, although some literature tend to prove the opposite (Phadtare et al., 2005). This promoter plays a role in transcription, though does not relate to the translation regulation (DSBox, 5’UTR). The CspA promoter is considered to be a strong promoter (Mitta et al., 1997).

Source of this part

Go to: https://www.ncbi.nlm.nih.gov/gene/948070 and in the 5'UTR. The Up element is an "AT-rich sequence (-47 to -38) upstream of the CspA -35 region. If you look now on the Cold-shock protein A gene on this region, you will find the sequence. If you take the CspA gene, you can then go to nucleotide number 3719890 (ACGGTT) to have the beginning of the 5'UTR. Then you need to go further to 3719843 (AAAATAATTG). You will notice that the sequence is indeed located from -47 to -38 from the 5'UTR beginning and is AT rich. Sequences of the cold-induced 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

Finding the UP element and the promoter was tricky and we needed certain amount of time to make sure we did not miss the sequence in the NCBI GenBank.

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

Sequence and Features