Naming Arabidopsis Syntaxins, a proposal

Anton A Sanderfoot sanderfo at pilot.msu.edu
Fri Jul 21 14:57:21 EST 2000


>From Anton Sanderfoot and Natasha Raikhel,

For an HTML version of this proposal, please see:

http://www.msu.edu/~sanderfo/nomenclature.htm


     With the near completion of the Arabidopsis genome sequence, a large number
of genes potentially encoding syntaxins have been found. Most have been found
to be represented by small gene families of a few to many members. Some of
these have been characterized previously and given various names, others are
noted only by the BAC designation. As many researchers now are beginning to
characterize these genes, some naming conflicts are bound to arise. To avoid
these potential problems, we would like to propose a systemic method for naming
the Arabidopsis syntaxins.
     Naming of the Arabidopsis syntaxins has been done in several different
ways. For example, KNOLLE, an existing genetic mutation was found to be encoded
by a syntaxin, and there may be reasons to maintain this name. Others have been
named with respect to the ability to complement mutations in yeast syntaxins
(AtPEP12, AtVAM3, etc.); though recent research may indicate these names could
be misleading with respect to the function in plants. Still others were named
in an attempt at a systemic nomenclature (AtSynt4 and AtSynt5), or were named
as "Syntaxin-related" (AtSYR1). Both to accomidate the new genomic annotations,
and to synchronize the nomenclature, we feel that a systematic method should be
used, and that this should be decided by the research community.
     Because we've found that the Arabidopsis syntaxins tend to come in small
gene families, and since this sequence homology among the gene family members
is significant, we would like to propose a system that indicates these gene
family members in some way, and yet is consistent with the rules of Arabidopsis
gene nomenclature.
     We propose to name each gene as "SYntaxin of Plants", then identifying each
gene with two numbers (e.g. AtSYP11). The first digit would reflect a
phylogenetic group, the second digit reflecting a member of that group.
Numbering would be based upon: 1) order of publication, or 2) depostion into
GenBank/EMBL/DDBJ of cDNA, or 3) appearance of annotated ORF from genomic
sequence.
     We have made groups of Syntaxins based upon sequence homology -- both to
themselves, and to syntaxins of other organisms:

Group 1 would include KNOLLE, SYR1, and 7 others; a group which shows most
homology to the plasma membrane type syntaxins of other eukaryotes.
Group 2 would include the PVC/Vacuolar syntaxins AtPEP12, AtVAM3, and AtPLP.
Group 3 would include the SED5-homologs (2 members).
Group 4 would include the TLG2-homologs (3 members).
And so on for other gene families.

For example:

KNOLLE is a member of the first group and was the first of this group to be
published, resulting in KNOLLE being "AtSYP11".

AtSYR1 was next of this group to be published and would be "AtSYP12".

AtPEP12 belongs to a second phylogenetic group and was first to be published,
resulting in "AtSYP21".

AtVAM3 was next from this group to be published, and is thus "AtSYP22".

Others would follow as listed in the table availible on the indicated web site
(http://www.msu.edu/~sanderfo/nomenclature.htm).

     It should be noted this system is based upon that currently in use for the
Arabidopsis Shaggy-like Kinases (see: Dornelas et al., 2000 Plant J 2000
Mar;21(5):419-29.)
     This list should be considered a "working proposal" and we intend it to be
an open disscussion for all members of the communtiy. We hope this will allow
for wide acceptance and use of the new nomenclature. Please forward comments to
this list, or to the Secretory Pathway mailing list (secpatwy at list.msu.edu) or
to directly to Anton Sanderfoot at sanderfo at msu.edu.

Once again, the entire table of syntaxins is available at the 
following address:

http://www.msu.edu/~sanderfo/nomenclature.htm


--
Anton Sanderfoot                  sanderfo at pilot.msu.edu
MSU-DOE Plant Research Lab           Phone: 517 353-3519
East Lansing, MI  48824-1312           Fax: 517 353-9168


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