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Harden, N., Clemens, J., Marygold, S.J. (2012.9.19). CG43741 nomenclature. 
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FBrf0219497
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On 19 Sep 2012, at Wed19 Sep  20:34 , James Clemens wrote:
Hi Steven,
I support a nomenclature adjustment.  The Ack genes in Drosophila and vertebrates present a nomenclature paradox.  FIrst off, I think I named the fly gene called Ack in a cell paper in 2000.  This designation was based on sequence similarities with a vertebrate enzyme called Activated Cdc42 kinase (ACK) which is now known as ACK1.  There is an ACK1 paralog called TNK1.  ACK1 and TNK1 share similar domain structures except TNK1 lacks a Cdc42/Rac interactive binding domain, the so called CRIB domain.  Fly Ack does not have a CRIB domain so arguably it appears to be more related to TNK1; however, Ack and ACK1 are more related from a sequence alignment/identity basis.  In fact, we find that ACK1, but not TNK1 and functionally rescue several fly Ack loss of function phenotypes.
Fly Ack also has a paralog as you know in PR2.  PR2 has a CRIB domain and is most closely related to ACK1 if you run a blast search, but the sequences surrounding the kinase activation loop suggest that PR2 my be the functional ortholog of TNK1.  Based on our findings, I would be tempted to rename the PR2 symbol as Tnk1, but I would have to do more sequence gazing to convince myself that is truly the best move.  For now, Ack-like might be the best bet name wise until a better function for PR2 is determined.
Cheers,
Jim
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On 19 Sep 2012, at Wed19 Sep  17:20 , nicholas harden wrote:
Dear Steven
I agree with both your naming suggestions. You might also want to consult with Jim Clemens at Purdue University.
Best regards
Nick Harden
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On Sep 19, 2012, at  6:36  AM, Steven Marygold wrote:
Dear Nicholas Harden,
FlyBase has some rather obscure nomenclature for the CG43741 gene:
its current symbol is "PR2" and it's current name is "Fak-like tyrosine kinase".
We would like to improve the current nomenclature to make things clearer and more accurate.
I see your lab has published at least two papers on the "PR2" gene:
Sem, K.P., Zahedi, B., Tan, I., Deak, M., Lim, L., Harden, N. (2002). ACK family tyrosine kinase activity is a component of Dcdc42 signaling during dorsal closure in Drosophila melanogaster.  Mol. Cell. Biol. 22(11): 3685--3697.
Zahedi, B., Shen, W., Xu, X., Chen, X., Mahey, M., Harden, N. (2008). Leading edge-secreted Dpp cooperates with ACK-dependent signaling from the amnioserosa to regulate myosin levels during dorsal closure.   Dev. Dyn. 237(10): 2936--2946.
So I wanted to get your expert view on this.
It looks like the "PR2" designation comes from this 1994 paper:
Ito, M., Matsui, T., Taniguchi, T., Chihara, K. (1994). Alternative splicing generates two distinct transcripts for the Drosophila melanogaster fibroblast growth factor receptor homolog.  Gene 139(2): 215--218.
As far as I can see, the Dmel gene was identified using a human beta-PDGFR probe, and so the "PR2" symbol stands for "PDGF Receptor isolate 2" or some such.
This isn't very useful or informative, especially since the Dmel gene appears to be most closely related to ACK genes.
I think the name "Fak-like tyrosine kinase" must also be derived from the Ito paper as it says:
"The DPR2 cDNA contained sequences similar to that of the catalytic domains of protein TyKs and were most closely related to fX, a non-receptor TyK (45.5% identity) (Schaller et al. 1992)."
In your papers, you state there are 2 ACK family members in Dmel - 'DACK' ('Ack' in FlyBase) and this 'PR2' gene.
I see that you do use 'PR2' in your papers, but I suspect you were following FlyBase convention rather that necessarily supporting the usefulness of this symbol?
Would 'Ack-like' be a more appropriate and more informative symbol (with 'Activated Cdc42 kinase-like' as the full name) for this gene?  Do you have an alternative suggestion?
Is there anyone else you know of that I should be talking to about this?
Many thanks for your time,
Steven.
--
Steven Marygold, Ph.D.
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