Team:Edinburgh/Collaboration

iGEM teams have always been a highly visible part of the synthetic biology community, and an important part of iGEM is contributing to that community. Thus, the relationship between our project and the projects of other teams, past and present, is of the highest importance.

The hub of our community's collective experience is the Parts Registry. During our work, we have discovered some useful information about several parts in the Registry. We have entered this information in the "experience" section of the relevant pages.

K415151

This part by MIT 2010 is supposed to encode FIXME

This information has been added to the Registry on the relevant [http://partsregistry.org/Part:BBa_K415151:Experience experience page].

K392008

This part by Osaka 2010 encodes a β-glucosidase from the bacterium Cellulomonas fimi. It is known to work in the lab of Chris French (Edinburgh's supervisor) and yet we discovered that an apparent frameshift is present near the start of the sequence.

Trieste's project this year also involves this part, and they too sequenced it and found the same "frameshift". Since a part with an early frameshift cannot possibly work, we looked for a different explanation.

Some 220 bases into the part, a 2nd ATG codon is found. This codon is in-frame and there is a plausible ribosome binding site (containing "gaagga") just upstream of it. We therefore believe that this 2nd ATG is the true start codon. The RBS would explain why the part can be expressed and work.

Indeed, the most recent [http://www.ncbi.nlm.nih.gov/nuccore/332337569?from=3105074&to=3106528 published sequence] of C. fimi β-glucosidase (labelled as such by [http://enzyme.expasy.org/EC/3.2.1.21 Expasy] though NCBI calls it a β-galactosidase) starts at the 2nd ATG codon of K392008. There are some other discrepancies between the published sequence and K392008 as well.

This information has been added to the Registry on the relevant [http://partsregistry.org/Part:BBa_K392008:Experience experience page].

Ice Nucleation Protein

We gratefully acknowledge UC Davis 2009, who synthesised an E. coli optimised version of Pseudomonas syringae Ice Nucleation Protein. We also acknowledge the help of this year's Leuven team, who also used Ice Nucleation Protein, and suggested alternative sources in case we needed them.