Subject: Gene renaming
I write to request a name change for a locus.
We have determined the enzymatic function for the gene previously
designated 'shanti' and will in all future publications refer to this
gene as: signal peptide protease, abbreviated spp. I was informed
that Helen Salz had previously used the designation spp for a SNF
protein, but she has graciously agreed to defer and to allow us to
use spp for the Drosophila signal peptide protease gene.
Thank you.
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Thomas Kornberg
Department of Biochemistry
University of California
San Francisco, CA 94143
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Subject: Re: Gene renaming
Dear Tom,
'shanti' (FBgn0031260) was named in
FBrf0134637 == Apionishev et al., 2001, Genes to Cells 6(3): 215--224
and although it was not a main focus of the paper the naming is
legitimate, and the name has been used in at least one later
publication \-
FBrf0167608 == Greil et al., 2003, Genes Dev. 17(22): 2825--2838
For FlyBase to change the symbol of shanti we would need you to
coordinate agreement with the Apionishev group (cc'd to FlyBase), with
an assurance that they would use spp in publications in the future.
.
Helen's gene is currently in FB as ' Spp:SNFs  Protein Partner'
(FBgn0038041). The upper case 'S' in is accordance with the community
gene naming rules 'Genes named after a protein product or other
molecular feature begin with an uppercase letter'
(http://flybase.bio.indiana.edu/docs/nomenclature/lk/nomenclature.html#1.1.).
The 'spp' choice for shanti (FBgn0031260) is not ideal. Helen's group
has used 'spp' for Spp (FBgn0038041) in the literature and so spp will
remain a synonym for Spp in FB even were spp to be adopted as a valid symbol
for shanti. This means that symbol/synonym searches for 'spp' would
return both Spp (FBgn0038041)and spp (FBgn0031260). This is not necessarily
the end of the world (there are other instances of this in FlyBase) but
it is something you should be aware of if you are going to proceed with
this name change. Where we have influence over symbols (i.e. when
people approach us for advice) we are steering people away from
symbols that differ from existing symbols only by capitalization, and
this is an example of that.
Of course the 'Genes named after a protein product or other molecular
feature begin with an uppercase letter' rule also implies that
FBgn0031260 (your spp i.e. shanti) should have an initial upper case
letter ('signal peptide protease' being a protein product name), but
that would bring it into conflict with Helen's Spp (FBgn0038041)....
You did say 'Helen ... has graciously agreed to defer' but didn't
suggest a new symbol for FBgn0038041.
.
These factors add up to a strong case for not choosing spp/Spp as symbols
for FBgn0031260/FBgn0038041, in fact for not renaming shanti at all.
However if you do want to pursue this I'd be happy to check out the relative
merits of any other suggestions you might have, before you approach the
Apionishev group.
With best regards,
Rachel.
for FlyBase.
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Subject: Re: Gene renaming
Good morning Rachel, Tom, Kevin etc.
The name Spp: SNF's protein partner (ie CG6525) has really only
appeared in fly base, and meeting abstracts. We have not yet published
our first paper on the characterization of this gene, and we are happy
to revert to CG6525 until we know more about its mutant phenotype.
Once we know more, we will try and come up with a clever name that is
not in use by anyone else.
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Helen Salz, PhD
Professor, Department of Genetics
Case Western Reserve University
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Subject: Re: Gene renaming
Dear Rachel-
I am not sure I follow all your arguments here, but I will try to
clarify the issues as I understand them.
Regarding the prior use of shanti by Apionishev et al, the work was
carried out in the Tanda lab and Soichi Tanda is in full agreement
with this name change. He is a collaborator in our work and a
co-author of the publication that identifies the protein product.
Our reasons for wanting to call this gene spp are the following: The
signal peptide protease enzyme is now and will be known as spp in
every other organism. There are already an extensive literature and
numerous reviews that use spp for the mammalian signal peptide
protease, so confusion would be inevitable if the Drosophila
community alone uses the name differently. It behooves us to have
Drosophila conform.
As Helen has confirmed, she has agreed to allow us to use spp despite
her prior use of it for the SNF protein partner her group is studying.
Please let me know if we need to do anything further to effect this
change. Our publication will be submitted in its final form to
Genetics today. Unless you advise otherwise, it will designate the
gene Spp, uppercase as you recommend.
Thank you.
Tom