response to "problems with lap nomenclature"

1
letters to the editor NATURE CELL BIOLOGY VOL 3 APRIL 2001 http://cellbio.nature.com E90 Problems with LAP nomenclature To the editor —It was recently proposed 1,2 that a group of cell-surface proteins with leucine-rich repeats (LRRs) and a PSD- 95/Dlg/ZO-1 (PDZ) domain, which have roles in epithelial cell shape and polarity, be collectively termed ‘LAP’ proteins (LRR and PDZ domain). This choice of name is inappropriate. 'LAP' is already used to designate two leucine aminopeptidase genes (LAP1 and LAP2), the herpesvirus latency-active promoter, and a liver acti- vating protein. Our direct concern is that LAP also designates a family of lamin- associated polypeptides (LAPs) in the nuclear envelope, which were reported in 1993. The term LAP has been used widely in the nuclear envelope literature, appear- ing in over 36 papers since 1993. The nuclear LAP1 and LAP2 genes encode alternatively spliced products (three and nine, respectively), many of which have distinct nuclear localizations and func- tions. Further lamin-associated proteins undoubtedly remain to be discovered, and interest in this area is high because of recent discoveries linking a LAP2-related protein, Emerin, to Emery–Dreifuss mus- cular dystrophy (EDMD), and linking lamin mutations to at least three different inherited diseases 4,5 . To avoid further confusion in the literature, we respectfully urge you to discuss these problems with our PDZ domain colleagues, and encourage them to choose a new, preferably four-let- ter name for LRR/PDZ domain proteins that does not duplicate a previously estab- lished name. Sincerely, Katherine L. Wilson*, Ricardo Benavente†, Brian Burke‡, Robert Craigie§, Roland Foisner¶, Kazuhiro Furukawa#, Larry Gerace**, Robert D. Goldman††, Yosef Gruenbaum‡‡, Crafford Harris§§, Christopher J. Hutchison¶¶, Georg Krohne†, Glenn E. Morris##, Henning Otto***, Amos J. Simon†††, Howard J. Worman‡‡‡ *John Hopkins School of Medicine, Baltimore, USA; †University of Würzburg, Germany; ‡University of Calgary, Canada; §National Institute of Health, Bethesda, Maryland, USA; ¶University of Vienna, Austria; #Niigata University, Japan; **Scripps Research Institute, California, USA; ††Northwestern University Medical School, Chicago, Illinois, USA; ‡‡Hebrew University of Jerusalem, Israel; §§R. W. Johnson Pharmaceutical Research Institute, San Diego, California, USA; ¶¶University of Durham, UK; ***Freie Universitat Berlin, Germany; ††† Chaim Sheba Medical Center, Tel Hashomer Israel; ‡‡‡Columbia University, New York, USA 1. Bilder et al. Nature Cell Biol. 2, E114 (2000). 2. Bryant, P.J. & Huwe, A. Nature Cell Biol. 2, E141–143 (2000). 3. Foisner, R. & Gerace, L. Cell 73, 1267–1279 (1993). 4. Wilson, K.L. Trends Cell Biol. 10, 125–129 (2000). 5. Bonne et al. Annals Neurol. 48, 170–180 (2000). Response To the editor — In calling attention to the several biomolecular entities whose names have been abbreviated ‘LAP’, Wilson et al. raise an important issue. Acronyms and similar abbreviations are beneficial for a term that is used repeatedly in a publica- tion; however, the existence of multiple entities that use the same abbreviation can cause confusion. It is for this reason that the universal standard of journals calls for explicit definition of an abbreviation at its first usage in a paper. This technique serves to dispel ambiguity that might arise. In selecting an acronym for the leucine- rich repeat and PDZ-domain-containing (LAP) family of proteins, we searched the PubMed database, as well as the curat- ed LocusLink nomenclature database (www.ncbi.nlm.nih.gov/LocusLink/), for previous uses of the abbreviation. As point- ed out by Wilson et al., LAP has been used for over 35 years to abbreviate the names of individual proteins (leucine aminopepti- dase, liver activating protein), a group of unrelated proteins that share binding part- ners (lamin-associated polypeptides), and an inherited human disorder (laryngeal adductor paralysis), as well as a gene-regu- latory element (latency-associated or active promoter). We have used this acronym in a distinct, non-overlapping context: to describe a structurally related protein fami- ly. Along with the initial explicit definition, the usage ‘LAP protein family’ serves to dis- tinguish the family of proteins that includes Densin-180, Scribble, Let-413 and ERBIN from other biomolecules. Because this is a distinct usage we will continue to apply it. David Bilder*, Daniel Birnbaum†, Jean-Paul Borg†, Jon Huibregtse‡, Mary Kennedy§, Michel Labouesse¶, Bernard Mechler#, Norbert Perrimon* *Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA; †U119 INSERM, Molecular Oncology, Marseille, France; ‡ICMB, University of Texas at Austin, Texas, USA; §Division of Biology, California Institute of Technology, Pasedena, California, USA; ¶IGBMC, CNRS/INSERM/ULP, Iukrich, France; #Developmental Genetics, Deutsches Krebforshungs-Zentrum, Heidelberg, Germany Nature Cell Biology would like to give our readers the opportunity to discuss subjects that have broad interest in the cell biology community. This section will publish brief letters that can be either linked to primary research, editorials, or commentaries published in Nature Cell Biology, or discuss other topics of widespread interest. Please see our website for further details http://nature.com/ncb/info/ guide_authors/cont.html#letters Call for Letters to the Editor LAP abbreviations (LocusLink nomenclature database: www.ncbi.nlm.nih.gov/LocusLink/) Hyperlipidemia atherosclerosis prone Leucine aminopeptidase genes (LAP1 and LAP2) Herpesvirus latency active promoter Liver activating protien Lamin-associated polypeptides Leucine-rich repeat and a PDZ domain Laryngeal adductor paralysis © 2001 Macmillan Magazines Ltd

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letters to the editor

NATURE CELL BIOLOGY VOL 3 APRIL 2001 http://cellbio.nature.comE90

Problems with LAP nomenclatureTo the editor —It was recently proposed1,2

that a group of cell-surface proteins withleucine-rich repeats (LRRs) and a PSD-95/Dlg/ZO-1 (PDZ) domain, which haveroles in epithelial cell shape and polarity, becollectively termed ‘LAP’ proteins (LRRand PDZ domain). This choice of name isinappropriate. 'LAP' is already used todesignate two leucine aminopeptidasegenes (LAP1 and LAP2), the herpesviruslatency-active promoter, and a liver acti-vating protein. Our direct concern is thatLAP also designates a family of lamin-associated polypeptides (LAPs) in thenuclear envelope, which were reported in1993. The term LAP has been used widelyin the nuclear envelope literature, appear-ing in over 36 papers since 1993. Thenuclear LAP1 and LAP2 genes encodealternatively spliced products (three andnine, respectively), many of which havedistinct nuclear localizations and func-tions. Further lamin-associated proteinsundoubtedly remain to be discovered, andinterest in this area is high because ofrecent discoveries linking a LAP2-relatedprotein, Emerin, to Emery–Dreifuss mus-cular dystrophy (EDMD), and linkinglamin mutations to at least three differentinherited diseases4,5. To avoid further confusion in the literature, we respectfullyurge you to discuss these problems withour PDZ domain colleagues, and encouragethem to choose a new, preferably four-let-ter name for LRR/PDZ domain proteinsthat does not duplicate a previously estab-lished name.Sincerely,

Katherine L. Wilson*, RicardoBenavente†, Brian Burke‡, Robert

Craigie§, Roland Foisner¶,Kazuhiro Furukawa#, Larry

Gerace**, Robert D. Goldman††,Yosef Gruenbaum‡‡, Crafford

Harris§§, Christopher J.Hutchison¶¶, Georg Krohne†,

Glenn E. Morris##, HenningOtto***, Amos J. Simon†††,

Howard J. Worman‡‡‡

*John Hopkins School of Medicine, Baltimore,USA; †University of Würzburg, Germany;

‡University of Calgary, Canada; §NationalInstitute of Health, Bethesda, Maryland, USA;

¶University of Vienna, Austria; #Niigata

University, Japan; **Scripps Research Institute,California, USA; ††Northwestern University

Medical School, Chicago, Illinois, USA; ‡‡HebrewUniversity of Jerusalem, Israel; §§R. W. Johnson

Pharmaceutical Research Institute, San Diego,California, USA;

¶¶University of Durham, UK; ***Freie UniversitatBerlin, Germany; ††† Chaim Sheba Medical

Center, Tel Hashomer Israel; ‡‡‡ColumbiaUniversity, New York, USA

1. Bilder et al. Nature Cell Biol. 2, E114 (2000).

2. Bryant, P.J. & Huwe, A. Nature Cell Biol. 2, E141–143 (2000).

3. Foisner, R. & Gerace, L. Cell 73, 1267–1279 (1993).

4. Wilson, K.L. Trends Cell Biol. 10, 125–129 (2000).

5. Bonne et al. Annals Neurol. 48, 170–180 (2000).

ResponseTo the editor — In calling attention to theseveral biomolecular entities whose nameshave been abbreviated ‘LAP’, Wilson et al.raise an important issue. Acronyms andsimilar abbreviations are beneficial for aterm that is used repeatedly in a publica-tion; however, the existence of multipleentities that use the same abbreviation cancause confusion. It is for this reason thatthe universal standard of journals calls forexplicit definition of an abbreviation at itsfirst usage in a paper. This technique servesto dispel ambiguity that might arise.In selecting an acronym for the leucine-rich repeat and PDZ-domain-containing(LAP) family of proteins, we searched the PubMed database, as well as the curat-ed LocusLink nomenclature database(www.ncbi.nlm.nih.gov/LocusLink/), forprevious uses of the abbreviation. As point-ed out by Wilson et al., LAP has been usedfor over 35 years to abbreviate the names ofindividual proteins (leucine aminopepti-dase, liver activating protein), a group ofunrelated proteins that share binding part-ners (lamin-associated polypeptides), andan inherited human disorder (laryngealadductor paralysis), as well as a gene-regu-latory element (latency-associated or activepromoter). We have used this acronym in adistinct, non-overlapping context: to

describe a structurally related protein fami-ly. Along with the initial explicit definition,the usage ‘LAP protein family’ serves to dis-tinguish the family of proteins that includesDensin-180, Scribble, Let-413 and ERBINfrom other biomolecules. Because this is adistinct usage we will continue to apply it.

David Bilder*, Daniel Birnbaum†,Jean-Paul Borg†, Jon Huibregtse‡,

Mary Kennedy§, MichelLabouesse¶, Bernard Mechler#,

Norbert Perrimon*

*Department of Genetics, Harvard MedicalSchool, Boston, Massachusetts, USA; †U119

INSERM, Molecular Oncology, Marseille, France;‡ICMB, University of Texas at Austin, Texas,

USA; §Division of Biology, California Institute ofTechnology, Pasedena, California, USA; ¶IGBMC,

CNRS/INSERM/ULP, Iukrich, France;#Developmental Genetics, Deutsches

Krebforshungs-Zentrum, Heidelberg, Germany

Nature Cell Biology would like togive our readers the opportunity to discuss subjects that have broad interest in the cell biologycommunity. This section will publish brief letters that can beeither linked to primary research,

editorials, or commentaries published in Nature Cell Biology, ordiscuss other topics of widespreadinterest. Please see our website forfurther detailshttp://nature.com/ncb/info/guide_authors/cont.html#letters

Call for Letters to the Editor

LAP abbreviations

(LocusLink nomenclature database:www.ncbi.nlm.nih.gov/LocusLink/)

• Hyperlipidemia atherosclerosis prone

• Leucine aminopeptidase genes(LAP1 and LAP2)

• Herpesvirus latency active promoter

• Liver activating protien

• Lamin-associated polypeptides

• Leucine-rich repeat and a PDZdomain

• Laryngeal adductor paralysis

© 2001 Macmillan Magazines Ltd