January 2010

Enzyme Aliases and Acronyms: What’s in a Name?

 

It’s not unusual to be listening to a seminar or reading or reviewing a paper or grant and feeling overwhelmed and confused by the aliases and acronyms used for enzymes. These enzyme identifiers seem to be increasing almost as rapidly as the number of papers published each year. Confusion often results from the fact that these names frequently bear no relationship to the actual activity or function of their enzyme. For example, how many people know the names of the enzymes represented by the aliases autotaxin, desnutrin, lipin, neuropathy target esterase, PatA/VipD, PTEN, SHIP2 and wunen? It’s pretty common to find a lipid scientist who doesn’t know that the common enzyme names for these aliases are lysophospholipase D, triacylglycerol lipase, phosphatidic acid phosphatase, phospholipase B, lysophospholipase A, phosphatidylinositol-3-phosphate phosphatase, phosphatidylinositol-3,4,5-trisphosphate phosphatase and lipid phosphate phosphatase, respectively. If lipid scientists don’t know what these aliases refer to, then how do we expect the general reader who is not a lipid aficionado to know?

There are a number of reasons why this practice got started. In many cases, the molecular function of a protein is unknown when it is discovered, and an alias is given based on a mutant phenotype or disease. In other cases, an investigator chooses a name, often with the admirable goal of making it easy to remember. No matter what the cause, rectifying this would go a long way to enhancing our ability to stimulate the enthusiasm and imagination of our colleagues.

Perhaps it would reduce confusion and increase clarity in the field at large if we changed the names of these enzymes to ones that reflect their activities. This, however, may not be straightforward. The names of most enzymes are derived from their substrates, products and the reactions they catalyze. Thus, many enzymes have a variety of names. For example, phosphatidate phosphatase 2, diacylglycerol pyrophosphate phosphatase and lipid phosphate phosphatase all refer to the same enzyme. Another problem is when an enzyme is more promiscuous than its name implies. For example, stearoyl-CoA desaturase implies the enzyme desaturates stearoyl (C18)-CoA. However, actually, the enzyme desaturates all acyl-CoA substrates from C14 to C20.

So how can we effectively and efficiently resolve this issue? Simply retaining the initial names of enzymes after their catalytic function is identified only perpetuates confusion in the literature. On the other hand, it is difficult to rename enzymes without upsetting the people who coined the aliases and acronyms, especially when those identifiers were established before the enzymatic functions of the proteins were known. For aliases, one solution is to refer to the enzyme activity followed by the alias in parenthesis or vice versa. The enzyme activity could be named according to standards set by the International Union of Biochemistry with emphasis on the thermodynamically favored reaction catalyzed. Similarly, acronyms should always be defined, especially when they are used in titles and abstracts. Whatever the solution, this may help to make lipid research more easily read and digested. In doing so, we will go a long way in conveying the excitement of lipid research.

*This article was written in response to a discussion in the forum on the Web site for the American Society for Biochemistry and Molecular Biology’s Lipid Research Division (www.asbmb.org/lipidcorner).

George M. Carman (carman@aesop.rutgers.edu) is a professor in the department of food science at Rutgers University. Daniel M. Raben (draben@jhmi.edu) is a professor of biological chemistry at the Johns Hopkins University School of Medicine.


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