Elspeth A. Bruford

The ABCs of solute carriers: physiological, pathological and therapeutic implications of human membrane transport proteins

The Human Genome Organisation (HUGO) Nomenclature Committee Database provides a list of transporter families of the solute carrier (SLC) gene series (see http://www.gene.ucl.ac.uk/nomenclature/). Currently, it includes 43 families and 298 transporter genes. This special issue features mini-reviews on each of these SLC families written by the experts in each field. A WEB site has been established (http://www.pharmaconference.org/slctable.asp) that gives the latest updates for the SLC families and their members as well as relevant links to gene databases and reviews in the literature. A list of all currently known SLC families, a discussion of additional SLC families and family members as well as a brief summary of non-SLC transporter genes is included in this introduction.

Guidelines for the nomenclature of the human heat shock proteins

The expanding number of members in the various human heat shock protein (HSP) families and the inconsistencies in their nomenclature have often led to confusion. Here, we propose new guidelines for the nomenclature of the human HSP families, HSPH (HSP110), HSPC (HSP90), HSPA (HSP70), DNAJ (HSP40), and HSPB (small HSP) as well as for the human chaperonin families HSPD/E (HSP60/HSP10) and CCT (TRiC). The nomenclature is based largely on the more consistent nomenclature assigned by the HUGO Gene Nomenclature Committee and used in the National Center of Biotechnology Information Entrez Gene database for the heat shock genes. In addition to this nomenclature, we provide a list of the human Entrez Gene IDs and the corresponding Entrez Gene IDs for the mouse orthologs.

Genenames.org: the HGNC resources in 2013

The HUGO Gene Nomenclature Committee situated at the European Bioinformatics Institute assigns unique symbols and names to human genes. Since 2011, the data within our database has expanded largely owing to an increase in naming pseudogenes and non-coding RNA genes, and we now have >33 500 approved symbols. Our gene families and groups have also increased to nearly 500, with ∼45% of our gene entries associated to at least one family or group. We have also redesigned the HUGO Gene Nomenclature Committee website http://www.genenames.org creating a constant look and feel across the site and improving usability and readability for our users. The site provides a public access portal to our database with no restrictions imposed on access or the use of the data. Within this article, we review our online resources and data with particular emphasis on the updates to our website.

A Unified Nomenclature for the Superfamily of TRP Cation Channels

The TRP superfamily includes a diversity of non-voltage-gated cation channels that vary significantly in their selectivity and mode of activation. Nevertheless, members of the TRP superfamily share significant sequence homology and predicted structural similarities. Currently, most of the genes and proteins that comprise the TRP superfamily have multiple names and, in at least one instance, two distinct genes belonging to separate subfamilies have the same name. Moreover, there are many cases in which highly related proteins that belong to the same subfamily have unrelated names. Therefore, to minimize confusion, we propose a unified nomenclature for the TRP superfamily.The current effort to unify the TRP nomenclature focuses on three subfamilies (TRPC, TRPV, and TRPM) that bear significant similarities to the founding member of this superfamily, Drosophila TRP, and which include highly related members in worms, flies, mice, and humans (Table 1)(Table 1). Members of the three subfamilies contain six transmembrane segments, a pore loop separating the final two transmembrane segments, and similarity in the lengths of the cytoplasmic and extracellular loops. In addition, the charged residues in the S4 segment that appear to contribute to the voltage sensor in voltage-gated ion channels are not conserved. The TRP-Canonical (TRPC) subfamily (formerly short-TRPs or STRPs) is comprised of those proteins that are the most highly related to Drosophila TRP. The TRPV subfamily (formerly OTRPC), is so named based on the original designation, Vanilloid Receptor 1 (VR1), for the first mammalian member of this subfamily (now TRPV1). The name for the TRPM subfamily (formerly long-TRPs or LTRPs) is derived from the first letter of Melastatin, the former name (now TRPM1) of the founding member of this third subfamily of TRP-related proteins. Based on amino acid homologies, the mammalian members of these three subfamilies can be subdivided into several groups each (Table 2Table 2 and Figure 1Figure 1) .Table 1Number of TRP Genes in Worms (C. elegans), Flies (Drosophila melanogaster), Mice, and HumansSubfamilyWormsFliesMiceHumansTRPC3376aaTRPV5255TRPM4188aTRPC2 is a pseudogene and is not counted.Table 2Nomenclature of the Mammalian TRP SuperfamilyNameGroupFormer NamesAccession NumbersTRPC11TRP1CAA61447, AAA93252TRPC1TRPC22TRP2X89067, AAD17195, AAD17196, AAG29950, AAG29951, AAD31453,TRPC2CAA06964TRPC33TRP3AAC51653TRPC3TRPC44TRP4CAA68125, BAA23599TRPC4TRPC54TRP5AAC13550, CAA06911, CAA06912TRPC5TRPC63TRP6NP_038866TRPC6TRPC73TRP7AAD42069, NP_065122TRPC7TRPV11VR1AAC53398OTRPC1TRPV21VRL-1AAD26363, AAD26364, BAA78478OTRPC2GRCTRPV3 (not assigned)TRPV42OTRPC4AAG17543, AAG16127, AAG28027, AAG28028, AAG28029,VR-OACCAC20703TRP12VRL-2TRPV53ECaC1CAB40138CaT2TRPV63CaT1AAD47636ECaC2CAC20416CaT-LCAC20417TRPM11MelastatinAAC13683, AAC80000TRPM22TRPC7BAA34700LTRPC2TRPM31KIAA1616AA038185LTRPC3TRPM43TRPM4H18835LTRPC4TRPM53MTR1AAF26288LTRPC5TRPM64Chak2AF350881TRPM74TRP-PLIKAAF73131Chak1LTRPC7TRPM82TRP-p8AC005538Indicated are the suggested gene and protein names, the groups within each subfamily, the former names, and accession numbers.Figure 1Phylogenetic Tree of the TRP SuperfamilyThe tree, which was adapted from Clapham et al., 2001 (Nat. Rev. Neurosci. 2, 387–396), was calculated using the neighbor-joining method and human, rat, and mouse sequences.View Large Image | View Hi-Res Image | Download PowerPoint SlideThe numbering system for the mammalian TRPC, TRPV, and TRPM proteins takes into account the order of their discovery and, in as many cases as possible, the number that has already been assigned to the genes and proteins (Table 2)(Table 2). In the case of the TRPV proteins, the numbering system is also based in part on the groupings of the TRPV proteins. New members of each subfamily will maintain the same root name and, with the exception of TRPV3, will be assigned the next number in the sequence. Currently, TRPV3 is unassigned to maintain the TRPV1/ TRPV2 and TRPV5/TRPV6 groupings and so that the former OTRPC4 could be renamed TRPV4. The next TRPV protein will be designated TRPV3.We hope this new nomenclature will add clarity to the field and simplify the naming of new members of the TRP superfamily. We recommend that accession numbers be used whenever it is necessary to unambiguously specify a given variant resulting from alternative mRNA splicing. Finally, this nomenclature has been approved by the HUGO Gene Nomenclature Committee and we recommend that this system be used in all future publications concerning TRPC, TRPV, and TRPM subfamily members.

The HUGO Gene Nomenclature Committee (HGNC).

The need for standard nomenclature in human genetics was recognised as early as the 1960s, and in 1979 full guidelines for human gene nomenclature were presented at the Edinburgh Human Genome Meeting (HGM) and subsequently published (Shows et al. 1979). The current Chair of the Human Gene Nomenclature Committee, Sue Povey, was elected at the HGM meeting in Heidelberg in 1996. Since then, under the auspices of the international Human Genome Organisations and with the acronym HGNC, we continue to strike a compromise between the convenience and simplicity required for the everyday use of human gene nomenclature and the need for adequate definition of the concepts involved. Numerical identifiers are satisfactory for computers, but when humans need to talk about a gene they prefer to use a name. Increasingly journals are requesting approved gene nomenclature before publication, although more standardisation in this respect would make a significant contribution to the annotation of the human genome (Povey et al. 1997; White et al. 1998). A recent analysis of networks of human genes from 10 million MedLine records illustrates the ingenuity currently required to extract information from the literature (Jenssen et al. 2001). The committee has grown from a single force (Dr Phyllis J. McAlpine) to the equivalent of five professional full-time staff, and operates through the Chair with key policy advice from an International Advisory Committee (IAC, http://www.gene.ucl.ac.uk/nomenclature/IAC.shtml). We also use a team of specialist advisors who provide support on specific gene family nomenclature issues (http://www.gene.ucl.ac.uk/nomenclature/advisors.html). Regular nomenclature workshops are held, frequently to coincide with the annual meeting of the American Society of Human Genetics (ASHG) and the HGM, to ensure that we are approving gene names in line with the needs of the scientific community. Guidelines for human gene nomenclature were last published in 1997 (White et al. 1977) and are also available online. New guidelines will be published in 2002 and a draft version can be inspected at http://www.gene.ucl.ac.uk/nomenclature/guidelines/draft _2001.html. For details of previous and future workshops see http://www.gene.ucl.ac.uk/nomenclature/workshops.html.

The SDR (Short-Chain Dehydrogenase/Reductase and Related Enzymes) Nomenclature Initiative

Short-chain dehydrogenases/reductases (SDR) constitute one of the largest enzyme superfamilies with presently over 46,000 members. In phylogenetic comparisons, members of this superfamily show early divergence where the majority have only low pairwise sequence identity, although sharing common structural properties. The SDR enzymes are present in virtually all genomes investigated, and in humans over 70 SDR genes have been identified. In humans, these enzymes are involved in the metabolism of a large variety of compounds, including steroid hormones, prostaglandins, retinoids, lipids and xenobiotics. It is now clear that SDRs represent one of the oldest protein families and contribute to essential functions and interactions of all forms of life. As this field continues to grow rapidly, a systematic nomenclature is essential for future annotation and reference purposes. A functional subdivision of the SDR superfamily into at least 200 SDR families based upon hidden Markov models forms a suitable foundation for such a nomenclature system, which we present in this paper using human SDRs as examples.

The HGNC Database in 2008: a resource for the human genome

The HUGO Gene Nomenclature Committee (HGNC) aims to assign a unique and ideally meaningful name and symbol to every human gene. The HGNC database currently comprises over 24 000 public records containing approved human gene nomenclature and associated gene information. Following our recent relocation to the European Bioinformatics Institute our homepage can now be found at http://www.genenames.org, with direct links to the searchable HGNC database and other related database resources, such as the HCOP orthology search tool and manually curated gene family webpages.

The HUGO Gene Nomenclature Database, 2006 updates

The HUGO Gene Nomenclature Committee (HGNC) aims to give every human gene a unique and ideally meaningful name and symbol. The HGNC database, previously known as Genew, contains over 22 000 public records with approved human gene nomenclature and associated information. The database has undergone major improvements throughout the last year, is publicly available for online searching at and has a new custom downloads interface at .

Renaming the DSCR1/Adapt78 gene family as RCAN: regulators of calcineurin.

Kelvin J. A. Davies,* Gennady Ermak,* Beverley A. Rothermel, Melanie Pritchard, Joseph Heitman, Joohong Ahnn, Flavio Henrique-Silva, Dana Crawford, Silvia Canaider,** Pierluigi Strippoli,** Paolo Carinci,** Kyung-Tai Min, Deborah S. Fox, Kyle W. Cunningham, Rhonda Bassel-Duby, Eric N. Olson, Zhuohua Zhang, R. Sanders Williams, Hans-Peter Gerber,*** Merce Perez-Riba, Hisao Seo, Xia Cao, Claude B. Klee, Juan Miguel Redondo, Lois J. Maltais, Elspeth A. Bruford, Sue Povey, Jeffery D. Molkentin,**** Frank D. McKeon, Elia J. Duh, Gerald R. Crabtree,§§§§ Martha S. Cyert, Susana de la Luna, and Xavier Estivill

Selenoprotein Gene Nomenclature

The human genome contains 25 genes coding for selenocysteine-containing proteins (selenoproteins). These proteins are involved in a variety of functions, most notably redox homeostasis. Selenoprotein enzymes with known functions are designated according to these functions: TXNRD1, TXNRD2, and TXNRD3 (thioredoxin reductases), GPX1, GPX2, GPX3, GPX4, and GPX6 (glutathione peroxidases), DIO1, DIO2, and DIO3 (iodothyronine deiodinases), MSRB1 (methionine sulfoxide reductase B1), and SEPHS2 (selenophosphate synthetase 2). Selenoproteins without known functions have traditionally been denoted by SEL or SEP symbols. However, these symbols are sometimes ambiguous and conflict with the approved nomenclature for several other genes. Therefore, there is a need to implement a rational and coherent nomenclature system for selenoprotein-encoding genes. Our solution is to use the root symbol SELENO followed by a letter. This nomenclature applies to SELENOF (selenoprotein F, the 15-kDa selenoprotein, SEP15), SELENOH (selenoprotein H, SELH, C11orf31), SELENOI (selenoprotein I, SELI, EPT1), SELENOK (selenoprotein K, SELK), SELENOM (selenoprotein M, SELM), SELENON (selenoprotein N, SEPN1, SELN), SELENOO (selenoprotein O, SELO), SELENOP (selenoprotein P, SeP, SEPP1, SELP), SELENOS (selenoprotein S, SELS, SEPS1, VIMP), SELENOT (selenoprotein T, SELT), SELENOV (selenoprotein V, SELV), and SELENOW (selenoprotein W, SELW, SEPW1). This system, approved by the HUGO Gene Nomenclature Committee, also resolves conflicting, missing, and ambiguous designations for selenoprotein genes and is applicable to selenoproteins across vertebrates.