Updated October 28, 1994 THE FOLLOWING IS AN UPDATE OF NOMENCLATURE RECOMMENDATIONS THAT APPEARED IN MOLECULAR PHARMACOLOGY 46:399-405 (1994). THERE ARE CHANGES IN THE PDE4D SUBFAMILY. ALSO AN ADDITONAL COLUMN NOTING DATE OF PUBLICATION IS INCLUDED. FINALLY ADDITIONAL NEW EMAIL ADDRESSES ARE GIVEN NOTE:THIS DOCUMENT WILL PRINT AND DISPLAY BEST IF 10 POINT COURIER TYPE IS USED. Table 1: CYCLIC NUCLEOTIDE PHOSPHODIESTERASE GENE FAMILIES Short PDE Isozyme Gene Number of Number of Evidence for Name Families gene products splice additional identified products members PDE1 CaM-dependent PDEs 3 9+ yes PDE2 cGMP-stimulated PDEs 1 2 yes PDE3 cGMP-inhibited PDEs 2 2+ yes PDE4 cAMP-specific PDES 4 15+ yes PDE5 cGMP-specific PDEs 2 2 possible PDE6 Photoreceptor PDEs 3 2 possible PDE7 HCP1-PDE * 1 1 possible * newly reported and likely to be renamed when unique regulatory properties are identified NOMENCLATURE A request was made at the April meeting in Newport Beach for volunteers to form a committee whose purpose will be to help organize and as necessary revise a standardized system of nomenclature for existing and newly discovered isozymes of cyclic nucleotide PDEs. Investigators who have volunteered to help edit this list include all of the meeting organizers as well as several other scientists. Their names and addresses are listed at the end of this article. It was decided initially to utilize the electronic "mailbox" mentioned in the previous section for this purpose. The major function for this mailbox would be to provide an easily accessible source for the most current data concerning the names and descriptions of all cyclic nucleotide PDEs that are already known. In addition, authors wanting to have any new PDEs that they discover listed would be able to contact one of the committee members and be assigned an appropriate name based on the set of criteria listed below. Suggestions for changes also can be made directly to any of committee members. The criteria for naming are summarized in the following example for a theoretical new entry into the LOCUS field of GenBank. FIGURE 1: GenBank/literature Nomenclature Gene (Capital Letter) | | Different Report | | example: HSPDE8A2A | | | | | Splice variant | | (Arabic numeral) | | | Gene family | (PDE + Arabic numeral) | Species (first 2 letters) The first two letters represent the species, for example HS for Homo sapiens. The next three letters plus an Arabic numeral designate the cyclic nucleotide phosphodiesterase gene family. The next letter represents the individual gene product within the family. The final Arabic numeral represents the splice variant and the final letter allows GenBank to assign a unique locus field designation based on when the entry was submitted and also to give different locus names to conflicting or incomplete sequences. It is hoped that most investigators will change their current GenBank LOCUS entries to this system and also will in the future use this nomenclature in the titles and abstracts of their manuscripts and in their GenBank submissions so that a common order for nomenclature may be instituted. This system should allow for future expansion ( at least until the number of gene families or splice variants exceeds 99 or the number of genes within any one gene family exceeds 26). It was also the consensus of discussion that more descriptive names based on regulation and function continue to serve a useful role in the text of most manuscripts. For examples, a paper on a PDE6 family member would be likely to include the terms "light activated or ROS or photoreceptor PDE" ; similarly one discussing the PDE2 family would be likely to include the terms "cGMP-stimulated PDE or cGS-PDE". A similar nomenclature system has been approved for adoption by the Human Genome Project Nomenclature Committee with the following differences. First, they omit the species since all are human sequences. Second, they use an asterisk followed by a second Arabic numeral to represent alleles rather than splice variants. The theoretical example shown above for a GenBank entry would be as follows in the Human Genome Entry. It is expected that the few current names in the Human Genome data bank will be changed to reflect this new nomenclature. Figure 2: HUMAN GENOME PROJECT NOMENCLATURE Gene (Capital Letter) | | example: PDE8A*2 | | | (Allele) | | Gene family (PDE + Arabic numeral) TABLE II CYCLIC NUCLEOTIDE PDE ISOZYMES Included in this table are most of the human, bovine and rodent cDNA references listed in GenBank or in recent literature references. Only those thought to be full length products or known to be catalytically active are listed. HuGP = Human Genome Project. Access Nnumer = GenBank Accession Number. HuGP NEW GB Old ACCESS ALTERNATE PUB DATE NAME NAME LOCUS NUMBER NAME (PDE1 GENE FAMILY) BTPDE1A1 59k CaM-PDE 8/91 BTPDE1A2 BOVCNPA M90358 61k CaM-PDE 8/91 BTPDE1B1A BOVCALPHOS M94867 63k CaM-PDE 7/92 RNPDE1B1A RATCAMPDE M94537 63k CaM-PDE MMPDE1B1A MUSPDE1B1 L01695 63k CaM-PDE 12/92 (PDE2 GENE FAMILY) BTPDE2A1 BOVCGMPCN M73512 cGS-PDE 10/91 (PDE3 GENE FAMILY) PDE3A HSPDE3A HUMGMPIPDI M91667 cGI-PDE 5/92 RNPDE3B RNCAMPPHA Z22867 cGI-PDE 10/93 (PDE4 GENE FAMILY)## RNPDE4A1A RATDUNCEA M26715 RD1 3/90 RNPDE4A1B RATPHOSF L27062 RPDE8 12/93 RNPDE4A2 RATDUNCEC M26717 RD2 3/90 RNPDE4A3 RATDUNCEB M26716 RD3 3/90 RNPDE4A?. RATPHOCNA M25348 ratPDE2 12/89 PDE4A HSPDE4A4 HUMPDEAA M37744 h-PDE1 1/91 PDE4A HSPDE4A5 HUMPDEA L20965 PDE46 12/93 PDE4A HSPDE4A5? HUMPDEC L20967 DPDE2,TM3 7/93 RNPDE4A5 RATPHOSA L27057 RPDE6 12/93 PDE4B HSPDE4B1 HUMPDEB L20966 TM72,DPDE4 7/93 RNPDE4B1 RATDPD J04563 DPD 12/89 PDE4B HSPDE4B2A HSPDE2A M97515 6/93 PDE4B HSPDE4B2B HUMPDEG L20971 PDE32 7/93 PDE4B HSPDE4B2C HUMCAMPB L12686 10/93 RNPDE4B2A RATPHOCAMB M25350 ratPDE4 9/89 RNPDE4B2B RATPHOSB L27058 RPDE18 12/93 PDE4C HSPDE4C1 HUMPDED L20968 DPDE1,PDE21 7/93 RNPDE4C1A RATPHOCN M25347 ratPDE1 9/89 RNPDE4C1B RATPHOSE L27061 RPDE36 12/93 RNPDE4D1A RATPHOCAMA M25349 ratPDE3.1 7/89 RNPDE4D1B RATPHOSD L27060 RPDE13 12/93 RNPDE4D2 RATPDE32 U09456 ratPDE3.2 7/89 PDE4D HSPDE4D3 HUMPDEF L20970 DPDE3,PDE43 12/93 RNPDE4D3A RATPHOSC L27059 RPDE3 12/93 RNPDE4D3B RATPDE33 U09457 ratPDE3.3 7/94 PDE4D HSPDE4D4 HUMPDEE L20969 DPDE3,PDE39 12/93 (PDE5 GENE FAMILY) BTPDE5A1 BOVPCGB8X L16545 cGB-PDE## 10/93 (PDE6 GENE FAMILY) PDE6A HSPDE6A1 HUMCGPRA M26061 ROS-PDEa 6/90 BTPDE6A1A BOVCGMP01 M27541 ROS-PDEa 10/87 BTPDE6A1B BOVCGPDAG M26043 ROS-PDEa 6/90 MMPDE6A1 MMPA X60664 ROS-PDEa 8/91 PDE6B HSPDE6B1 HSCGMPPM X66142 ROS-PDEb 8/93 BTPDE6B1 BOVCGMP J05553 ROS-PDEb 6/90 MMPDE6B1A MUSPDE X55968 ROS-PDEb 6/91 MMPDE6B1B MMPB X60133 ROS-PDEb 8/91 BTPDE6C1 BOVPDE M37838 COS-PDEa' 6/90 (PDE7 GENE FAMILY) PDE7A HSPDE7A HUMCAMPHOS L12052 HCP1 ## 8/93 ## Not full length TABLE III: NOMENCLATURE COMMITTEE ADDRESSES. Dr. Joe Beavo Dr. Graeme B. Bolger Dept. of Pharmacology, SJ-30 University of Utah Medical Center Univ. of Washington Division of Hematology/Oncology School of Medicine 50 North Medical Center Drive Seattle, WA 98195 Salt Lake City, UT 84112 206-543-4006 Office 801-582-1565 Office 206-685-3822 FAX 801-583-9624 FAX beavo@u.washington.edu Graeme.Bolger@m.cc.utah.edu Dr. Marco Conti Dr. John Colicelli Stanford University UCLA Department of GYN/OB, Dept. of Biological Chemistry 300 Pasteur Drive Los Angeles, CA Stanford, CA 94305-5317 415-725-2452 Office 310-206-7800 Office 415-725-7102 FAX 310-825-9433 FAX Marco.Conti@Forsythe.Stanford.edu colicelli@lbes.medsch.ucla.edu Dr. Jackie D. Corbin Dr. Ken Ferguson Vanderbilt Univ. ICOS, Inc School. of Medicine 22021 20th Ave. S.E. Dept. of Physiology Bothel, WA 98021 Nashville, TN 37232 485-1900 Office 615-322-4384 Office 485-1911 FAX 615-343-0490 FAX KEN_FERGUSON@smtpgate.icos.com CORBIN@lhmrba.hh.vanderbilt.edu Dr. Rodolphe Fischmeister Dr. Richard J. Heaslip Lab. de Cardiologie et Molec. Wyeth-Ayerst Research 5, Rue Jean-Baptiste Clement, Div. of Immunopharmacology Univ. de Paris-Sud C.N. 8000 Chatenay-Malabry Cedex, Princeton, NJ 08543 F, 92296 FRANCE 33-1 46 83 57 71 Office 908-274-4209 Office 33-1 46 83 54 75 FAX 908-274-4738 FAX fisch@sinaps.inserm-vjf.fr heslpraa@prince.mm.wyeth.com Dr. Miles D. Houslay Dr. Vincent C. Manganiello University of Glasgow Head, Section on Biochem. Physiol. Dept of Biochemistry NIH, Building 10, Rm 5N-307 Glasgow, Scotland G12 8QQ Bethesda, MD 20892 UNITED KINGDOM 301-496-5194 Office 44-41-339-8855 Office 301-402-1610 FAX 44-41-330-4620 FAX vmango@helix.nih.gov gbca29@udcf.gla.ac.uk Dr. Steven J. Pittler Dr. Sam Strada Dept. of Biochem. & Mol Biol. Dept. of Pharmacology, MSB 3130 Univ. of S. Alabama Med. Sch., U. South Alabama Col. of Med. MSB 2158 Mobile, AL 36688-0001 Mobile, AL 36688 205-460-6861 Office 205-460-6497 Office 205-460-7134 FAX 205-460-6798 FAX pittlers@sungcg.usouthal.edu sstrada@jaguar1.usouthal.edu Dr. Theodore J. Torphy SmithKline Beecham Dept. of Pharmacology, L-532 PO Box 1539 King of Prussia, PA 19406-0939 215-270-6821 Office 215-270-5381 FAX Theodore_J_Torphy%notes@sb.com