Cite fluorescent protein origins

[ewallace]

mCherry - cite Shaner 2004

@j-aux I know mCherry is used in the YeastFab 2015 paper, what should we cite for the choice of yeast codon-optimized versions of that?

mTurquoise2 - cite Goedhart 2012
I checked that this sequence is mTurquoise2, which differs from mTurquoise by an I146F substitution (search for KLEYNYFSDN)

Again, where is the mTurquoise2 coding sequence from?

[ewallace]

Note - I checked and these proteins have 30% amino acid identity, so that number is going in the draft.

And I added the Shaner 2004 and Goedhart 2012 references in commit 3897bc0

[j-aux]

For the mTurquoise2 we used, it was amplified from Lee 2015. For the mCherry we used, it was amplified from Guo 2015

[ewallace]

Thanks! Lee 2015 doesn't say how they designed their codons or if it was synthesized/amplified, as far as I can tell. I will email the corresponding authors about that.

[ewallace]

Is the mCherry sequence the same as that used in Sharon 2012, i.e. the Segal lab dual-reporter plasmid?

[j-aux]

Yes. Guo 2015 amplified from Sharon 2012.

They amplified from 'pAG60-TEF2-Cherry plasmid' from the Breslow 2008 paper but I haven't figured out what their mCherry is made from.

[ewallace]

Huh. Maybe that explains why the mCherry is so ridiculously GC-rich?

[ewallace]

We still need to add references to the codon encodings used for these to the draft.

[DimmestP]

I will compare these sequences to check where we got them from (July 6th Meeting)

[ewallace]

They amplified from 'pAG60-TEF2-Cherry plasmid' from the Breslow 2008 paper but I haven't figured out what their mCherry is made from.

I checked the supplementary info of Breslow 2008, and it uses dTomato not mCherry. So maybe we give up on this? We use fluorescent proteins that have been used before and we cite where we got them. But we haven't even tried to control for codon usage.

[ewallace]

After discussing with @DimmestP , commit 5c64604 adds immediate references. That is good enough for me. Closing as we merge #199