Subject: Help FlyBase: Lim genes
Dear Beth,
I am a curator of FlyBase working at the Cambridge, England, site with
Prof. M. Ashburner.
In our genes file we have 6 LIM-only genes.
Find shortened entries below:
\*a Lim1
\*i DmLIM-1
\*x FBrf0079460 == Stronach et al., 1995, A. Conf. Dros. Res. 36: 321B
\*x FBrf0067663 == Stronach et al., 1994, A. Conf. Dros. Res. 35 Addendum: 16
\*a Lim2
\*i DmLIM-2
\*i Mlp1
\*x Cell 79, 221--231 (1994)
\*x FBrf0079460 == Stronach et al., 1995, A. Conf. Dros. Res. 36: 321B
\*x FBrf0067663 == Stronach et al., 1994, A. Conf. Dros. Res. 35 Addendum: 16
\*g X81192
\*a Lim3
\*i DmLIM-3
\*x FBrf0079460 == Stronach et al., 1995, A. Conf. Dros. Res. 36: 321B
\*x FBrf0067663 == Stronach et al., 1994, A. Conf. Dros. Res. 35 Addendum: 16
\*a Lmo
\*i Rho: Rhombotin
\*c 17C1--17C2
\*x FBrf0052759 == Boehm et al., 1990, Oncogene 5: 1103--1105
\*x Oncogene 11, 1283-1290 (1995)
\*g X83037
\*g X54988
\*a Mlp60A
\*g X91244
\*i Mlp1
\*x Cell 79, 221--231 (1994)
\*a Mlp84B
\*g X91245
I was hoping you would be able to help with three main queries concerning
these genes. If you could also consult Dr Beckerle about these queries I
would be very grateful (we have no entry for Beckerle in the FlyBase people
directory).
1)
On a previous cruise of the LIM genes I read this statement from the
introduction of Zhu et al, 1995, Oncogene 11: 1283:
'Lmo is the agreed new name of the LMO (LIM-only) genes as decided at the
'Workshop on LIM proteins and LIM domains' (Strasbourg, 1995)'.
On the basis of this have you renamed your genes Lim-1, Lim-2 or Lim-3 to
have Lmo designations? If you are considering this please keep in mind
that we already have Lmo as a FlyBase accepted gene symbol (included in
the above list).
2)
We know that Lim-2 and Mlp60A are the same gene (from ADRC 36: 321B and
amino acid homology). We have not merged these genes yet as we are unsure
what to name the merged gene.
Prof Ashburner prefers the Mlp designation as it distinguishes these genes
from the non-muscle LIM-only proteins. But the Lim-2 symbol should be
used if we conform to the rules of precedence. But if you are using Lmo
designations then we should use this.
HELP!
On the same lines do you know if Lim-1 or Lim-3 are homologous to Lmo (on
the basis of protein homology and cytological location) or if either are
homologous to Mlp84B?
3)
The sequence record for Mlp60A and Mlp84B states Stronach B.E., Siegrist
S.E., Beckerle M.C. (Unpublished). Do you have the details for this
publication now, if so could you please give me the information?
Many thanks for any help you can offer,
Eleanor Whitfield
FlyBase
>
Subject: Re: Help FlyBase: Lim genes
Dear Eleanor
Sorry it took so long to reply but I wanted to converse with my advisor
before writing back.
Here's how we see it.
1) Lim1=DmLIM-1... we isolated this sequence based on homology to chicken
zyxin. It has three C-terminal LIM domains. It maps to 102EF. We were
not sure if it is the true zyxin homolog, so referred to it as DmLIM-1 (for
the first LIM gene we isolated). We don't particularly like this
designation and I think it would not be wise to call it LIM1 because it
might get confused with vertebrate LIM-1's which are LIM-homeodomain
proteins, clearly not homologs of this gene. So we have a dilemma,
nothing is published formally yet about this gene, perhaps you can
advise... should we call it drosophila zyxin, or LIM102EF for convention ,
or something else like  ZRP:zyxin  related protein. We have no expression
data yet.
2) DmLIM-2=Lim2=Mlp1=Mlp60A... this gene has a single LIM domain and is
clearly expressed in muscle. We prefer the Mlp designation. We submitted
sequence under the name Mlp60A, thinking this was similar to established
conventions for naming genes in Drosophila...e.g.Actins plus their map
positions. Our competitors, however, published first in CELL 79, 221-231,
and chose to call the gene Mlp1... we have submitted our own paper and call
the gene Mlp1 deferring to their name...Again, please advise. We are not
interested in keeping the 'Lim2' name. Also, this gene does contain only
LIM domains but is clearly quite different from the LMO/Rhombotin family,
so we prefer not to use the LMO designation.
3) DmLIM-3=Lim3=Mlp84B....This gene is very similar to Mlp1 in sequence,
but it has five LIM domains and clearly maps to a different location,
84BC. We believe that it is a family member with Mlp1, and it is
definitely also expressed in muscle. We have chosen to submit the sequence
as Mlp84B, like Mlp60A. This gene is also described in our paper which is
submitted and being reviewed right now. I suppose we could call it Mlp2,
but this adds just another name, so what do you think??? Stick with
Mlp84B, NOT Lim3 or DmLIM-3? Again, we do not feel the LMO designation is
appropriate as this gene is related to Mlp1 not Rhombotin.
Well, I hope this is helpful. We are willing and eager to work out a good
naming system for these LIM genes according to established practice. If
you need any further information, please don't hesitate to write again.
and perhaps we can decide on something for the 4th chromosome gene that
is related to vertebrate zyxin.
Thanx for considering this issue with us and for your patience.
Sincerely,
Beth Stronach
Dept of Biology
University of Utah
Salt Lake City, Utah 84112
>
Subject: Re: Help FlyBase: Lim genes
Hi Beth,
In answer to each section:
>1) Lim1=DmLIM-1... we isolated this sequence based on homology to
>chicken zyxin. It has three c-terminal LIM domains. It maps to 102EF.
>We were not sure if it is the true zyxin homolog, so referred to it as
>DmLIM-1 (for the first LIM gene we isolated). We don't particularly like
>this designation and I think it
>would not be wise to call it LIM1 because it might get confused with
>vertebrate LIM-1's which are LIM-homeodomain proteins, clearly not
>homologs of this gene. So we have a dilemma, nothing is published
>formally yet about this gene, perhaps you can advise... should we call it
>drosophila zyxin, or LIM102EF for convention , or something else like
> ZRP:zyxin  related protein. We have no expression data yet.
A prefix to indicate that the gene is from Drosophila, e.g. D, Dm, Dmel or
Dro is redundant in the database and is, therefore, not used in valid gene
names. If you are concerned that the symbol Lim1 suggests homology to
vertebrate Lim-1's then using the cytology as a suffix would be
acceptable. In later formal publications the valid name would be Lim102EF,
this would be the valid symbol in FlyBase with the synonyms Lim1 and
DmLim-1. Please note the nomenclature: genes named after a protein product
begin with an uppercase letter, i.e Lim102EF NOT LIM102EF.
Also, could you please confirm that this gene, that does contain only LIM
domains, is different from Lmo and therefore that you should not use an Lmo
designation? If it is a member of the Lmo family the valid symbol could
be Lmo102EF?
>2) DmLIM-2=Lim2=Mlp1=Mlp60A... this gene has a single LIM domain and
>is clearly expressed in muscle. We prefer the Mlp designation. We submitted
>sequence under the name Mlp60A, thinking this was similar to established
>conventions for naming genes in Drosophila...e.g.Actins plus their map
>positions. Our competitors, however, published first in CELL 79,
>221-231, and chose to call the gene Mlp1... we have submitted our own
>paper and call the gene Mlp1 deferring to their name...Again, please
>advise. We are not interested in keeping the 'Lim2' name. Also, this
>gene does contain only LIM domains but is clearly quite different from
>the LMO/Rhombotin family, so we prefer not to use the LMO designation.
At present we have both Lim2 and Mlp60A. Mlp60A was used over and above
Mlp1 as we did not want to infer homology to the vertebrate Mlp1 gene, so
you were correct in using the Mlp60A symbol. Based on your information we
shall merge these genes and the valid symbol for both will be Mlp60A (as
you and also Prof. Ashburner prefer), synonyms Lim2 and DmLIM-2. If it is
not too late maybe you could change the designation from Mlp1 to Mlp60A in
your submitted paper?
>3) DmLIM-3=Lim3=Mlp84B....This gene is very similar to Mlp1 in sequence,
>but it has five LIM domains and clearly maps to a different location,
>84BC. We believe that it is a family member with Mlp1, and it is
>definitely also expressed in muscle. We have chosen to submit the
>sequence as Mlp84B, like Mlp60A. This gene is also described in our paper
>which is submitted and being reviewed right now. I suppose we could call
>it Mlp2, but this adds just another name, so what do you think???
>Stick with Mlp84B, NOT Lim3 or DmLIM-3? Again, we do not feel the LMO
>designation is appropriate as this gene is related to Mlp1 not Rhombotin.
I'm sure you will know the answer to your question now based on my previous
comments, please use Mlp84B for the valid symbol (not Mlp2). In FlyBase we
have both Lim3 and Mlp84B, I shall merge these genes and the valid symbol
will be Mlp84B with synonyms DmLIM-3 and Lim3.
The only outstanding point from my original communication, which I shall
revise based on information already given, is:
Do you know if Lim1 and Lmo belong to the same family and therefore Lim1
should have an Lmo designation?
(I have asked this in the above text for point 1)
Also I am assuming the paper Stronach B.E., Siegrist S.E., Beckerle M.C.
(Unpublished) is that which is being reviewed as we speak and therefore you
do not know the publication details yet?
Considering the size of my original message I have to thank you (and your
advisor) for a very thorough coverage and I eagerly await your reply!
Many thanks.
Eleanor Whitfield
>
Subject: Re: LIM gene nomenclature
Well, I believe Lim102EF not to be related to Lmo/rhombotin aside from
having LIM domains...that is, it is part of a huge superfamily of LIM
proteins but is not a close family member of rhombotin/Lmo.
So in other words, we don't wish to refer to this gene with an Lmo
designation, and we hereafter refer to it as Lim102EF
also, to clarify, we don't have any further publication details on the
Stronach et al paper. But perhaps any day I will hear back, and would be
happy to update you with the information, also I will take into
consideration your suggestion to call the gene Mlp60AB instead of Mlp1 in
the paper.
Thanks again, Beth Stronach
>
Subject: Re: LIM gene nomenclature
Hi Beth,
Thanks for your prompt reply.
I shall curate the new information you have given me as a personal
communication from yourself and look forward to receiving the publication
information on the new paper. We curate 75 journals, of which we have a
top ten that we are concentrating on getting upto date. I imagine your
paper will be in one of these journals.
Eleanor Whitfield