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A PERSONAL VIEW
Division of Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
Address for reprint requests and other correspondence: L. Nordquist, Div. of Integrative Physiology, Dept. of Medical Cell Biology, Uppsala Univ., Biomedical Centre, Box 571, Uppsala 751 23, Sweden (e-mail: Lina.Nordquist{at}mcb.uu.se)
PROTEINS, activators, transcription factors, genes, and more proteins. Life sciences can be complicated enough without getting into the names of all its Dalton-scale participants. For many students, composing a project plan or writing a paper is rather like learning a foreign language. Senior researchers master the excellent National Center for Biotechnology Information, Protein Information Resource, and other databases (1, 2), and, with the Rosetta stone, Champollion et al. were finally able to decipher the hieroglyphs, but what about the students? Where is their Rosetta stone?
Standard nomenclature of genes and proteins is slightly confusing more often than not. Although as a standard, the gene itself is typed in italic and the gene product is typed with a capital letter and in normal typeface, this is not where the story ends. First, the nomenclature varies between organisms, meaning just typing their names may require some research. Second, the names themselves may have their roots in origin, function, appearance, relationship to other molecules, or a combination thereof. So many names, and nowhere is an easy-to-find and easy-to-use translator to be found. A small number of researchers, such as Dr. Jonathan Swinton (6), have taken matters into their own hands and written interesting as well as entertaining online columns on the proteoetymology of words relevant to their field of research, but these Samaritans exempt, there are few sources of information to find.
There are thousands of abbreviations, and although their whole purpose is to simplify communication, some names appear more confusing than explaining. Generally, "K" is for kinase and "P" for phosphorylating, but that is not necessarily the case. Names may require competence in anything from history to Japanese, as is the case with JNK, or "ju-nana kinase," as it appears to have been originally named (3). Ju-nana is Japanese for seventeen, and, quite logically, JNK was isolated from avian sarcoma virus 17. Giving a full name for an abbreviation may be lengthy but is a reasonable requirement for the acceptance of a paper, to say the least. But what is an abbreviation? At times it is not clear whether there is an actual abbreviation or just a somewhat curious full name. My own favorite protein, C-peptide, is likely named as the connecting peptide between the insulin A (
) and B (β) chains but could just as well simply be the C chain. Another example is the key signaler AKT, whose origin dates to more than half a century before AKT itself was first reported, first to AKR mice, then thymoma cell line AKT-8, and, most recently, to the T-8 virus, which became the finding place of AKT (5, 6). The letter "A" was the stock of mice, and "K" could be the strain, but is this an abbreviation? And if not–how should you know?
Finally, to the veritable challenge: multiple names. AKT, as many others, also goes under another name, protein kinase B (PKB) (4). Not that this is unexpected. As technology speeds up the discovery rate of proteins and compounds, there are numerous examples of concomitant, independent characterization leading to several acceptable names. This means not even a thorough study of relevant papers will necessarily produce a correct explanation of the abbreviation in question, and even less so full information of the field of study. As an example, mitogen-activated protein kinase (MAPK) appears to have been originally abbreviated from "microtubule-associated protein kinase," later renamed "extracellular signal-regulated kinase" (ERK), before resuming to MAPK, this time as the name of the kinase superfamily (6, 8). As for the MAPK gene, it is sometimes referred to as "protein kinase mitogen-activated, 1." We are simply not in Kansas anymore.
There is a linguistic jungle out there, and it may well discourage students from pursuing a life science career. So what can the scientific community do? Although proper names, or even a single name per molecule, can hardly be expected at the time of discovery, we should put effort into rapid, reasonable, and logical naming of novel substances. Foremost, a Rosetta stone could do the trick. My hope is that in the near future, any student's search for a protein will generate hits not only on the name used in the search but retrieve all matches on that biological concept, similar to the system developed by Tsuruoka et al. (7). We should come up with an easy-to-use (and understand), accessible database for compounds and their origin: the Compilation of the Bricks of Life, or The Online Life Science Dictionary if you prefer. In the meanwhile, we owe it to our younger colleagues to give clear definitions of all substances mentioned in our publications. For the sake of students, investigators, and not the least for future research: I am convinced it will allow many students more time in the laboratory and less frustration hunting for the full names and origins of senior researchers' babies.
Received for publication March 3, 2008. Accepted for publication July 29, 2008.
REFERENCES
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