ABSTRACT
The nomenclature of Mitogen Activated Protein Kinases (MAPKs) takes different formats composed of symbols, prefixes, suffixes, or descriptive acronyms of their functions that sometimes lead to confusion and make the indexed information redundant and inconsistent. To avoid such redundancy and reduce confusion, a curation of the terminology of MAP kinase families, and that of other protein families that present similar nomenclature issues, is required. Some arguable suggestions are presented here toward this goal.
Mitogen activated protein kinases (MAPKs) are large signaling protein families involved in cell responses to different types of biotic and abiotic stresses.Citation1-7 In the model plant Arabidopsis thaliana, four MAP kinases families have been describedFootnotea : the MAP kinases family (also known as MAPK or MPK family), the MAPK kinase family (also known as MAPKK, MAP2K, MKK, or MEK), the MAPK kinase kinase family (also known as MAPKKK, MAP3K, MEKK, or MKKK), and the MAPK kinase kinase kinase (also known as MAPKKKK or MAP4K). As seen, the names of MAP kinase families take different formats and the nomenclature of their members also take multiple alternative names composed of symbols and serial numbers prefixed with an organism name or suffixed with a number of “K” (for “kinase”) to refer to the kinase family a protein belongs to (for e.g., “MKK”, MAP2K and “MAPKK” refer to the MAP kinase kinase family) or with acronyms of the protein functions (for e.g., “SAPK” for “stress-activated protein kinase” and “WIPK” for “wound-induced protein kinase”, etc.).
As such, many MAP Kinases have several names that can confuse the reader and mislead the investigator (for e.g., AtMPK6 has the following aliasesFootnoteb : ATMPK6, MPK6, ATMAPK6, F18O19.10, MAP kinase 6, and MAPK6). MAP2K1, MPKK1, MKK1 or MEK1” can also refer to one and same MAPKK protein. In mammals, MAP kinases nomenclature is even worse where some MAP kinases have up to more than 10 aliases scattered between different formats such as MAPKn, ERKn, PnnERK and PnnMAPK, etc., where n is an Arabic serial number. For example, the human mitogen-activated protein kinase-1 has the following alternative namesFootnotec : MAPK1, ERK; p38; p40; p41; ERK2; ERT1; ERK-2; MAPK2; PRKM1; PRKM2; P42MAPK; p41mapk, and p42-MAPK (see other examples for MAPK3Footnoted , MAPK8Footnotee , and MAPK9Footnotef among others). If a scientist uses a given gene name (say AtMPKK1) and another scientist uses another name (say MKK1) and a third scientist uses a third name (say MEK1) for the same gene, the data related to this gene can be redundant, incomplete or inconsistent depending on its name being used by investigators. Furthermore, when talking about “MAP kinases” or “MAPKs” it is still tricky to know straightforwardly whether we mean the family MAPK (with one “K”) or all the MAP kinase families as there is no formal or clear rule on this issue. In other words, MAPKs and MAP kinases are used interchangeably to refer to either all the mitogen-activated protein kinase families or to one family only, the MAPK family with one “K”. For convenience, MAP kinases are used here to refer to all the MAP kinase families and MAPK to refer to the MAPK family.
In my view, multiple terminologies of MAP kinases are unnecessary as they may lead to confusion and make the indexed information overwhelming in biological databases such as those of the National Center for Biotechnology Information (NCBI) that hosts about 67 online databasesFootnoteg in health, bioinformatics and biotechnology information, ranging from genes to genomes, cells to organisms, and structures to functions so that using multiple or alternative gene or protein names could be misleading.
To remove obsolete and redundant information on MAP kinase families and to keep the indexed data easily retrievable, comparable and interpretable, it should be time for curation and standardization of gene and protein nomenclature of MAP kinases, and other gene families that present similar and multiple terminology issues. Short terminology versions such as MPKn or MAPKn are good options to name MAP kinases members but such an approach cannot be applied to all the MAP kinase families in all species unless it is specified all the time that a gene or a protein of interest is meant in this or that species otherwise it will be difficult to distinguish to which species a gene or protein name belongs to. MPKn (for e.g., MPK1, MPK2, MPK3, etc.) are generally used to name MAPKs in Arabidopsis and MAPKn (i.e., MAPK1, MAPK2, etc.) are usually used to name MAPKs in other species (human, mouse, and so on), though this is not a formal rule as MAPKn formats are sometimes also used to name MAPKs in Arabidopsis. Therefore, such an approach lacks scientific rigor and leads to confusion and time wasting when there is a need to search and find a gene or protein of interest amid an increasingly elongated lists of genes and genomes being sequenced and/or updated continuously. A more systematic, standardized, and less ambiguous approach is thus required to name MAP kinases in all species to remove such ambiguity. Here are some arguable suggestions toward this goal:
| 1) | Using MAPKn to (re)name all the members of the MAPK family in all species but not using MPKn for MAPKs in Arabidopsis and MAPKn in animals or both symbols in either one as is currently the case (“n” is an Arabic serial number to distinguish proteins each from others). | ||||
| 2) | Using MAPKKn to (re)name all the members of the MAPK kinases’ family. In my opinion, the symbol “2K” should be avoided in a formal nomenclature of MAPKKn because protein names with “2K” such as MAP2K1, MAP2K2, MAP2K3, etc., can be confounding as the number “2” before the “K” could confusingly refer to the preceding “P” as well as to the next “K” in the used form “MAPnK”. By contrast, the symbols MKK and MEK are already abbreviations of the abbreviations of MAP kinases, so they should also be avoided for the sake of clarity and less ambiguity. | ||||
| 3) | Using MAPKKKn to (re)name all the members of the MAPKK kinases’ family in all species. Similarly to the symbol 2K above, the symbols “3K” here should also be avoided in a formal nomenclature of the MAPKKKn family because protein names with “3K” such as MAP3K1, MAP3K2, MAP3K3, etc., can be confounding as the number “3” before the “K” could refer either to the preceding “P” or to the next “K”. By contrast, protein names with MEKK, MP3K, and MAP3K are abbreviation of the abbreviations that should also be avoided for the sake of clarity and less ambiguity. | ||||
| 4) | Using MAPKKKKn to (re)name the members of the MAPKKK kinases’ family in all species. Names with the symbol “4K” such as MAP4K1, MAP4K2, etc., should be avoided as the number “4” in “MAP4K1” format can be confusingly associated with the preceding “P” or with the next “K”. | ||||
| 5) | In all the cases above, the abbreviation of the scientific name of species should be used as a prefix in the terminology of all the MAP kinases so that it would be easier to recognize to which species a MAP kinase gene or protein belongs to when mentioned or retrieved in specialized biological databases. | ||||
Finally, these suggestions remain, of course, debatable. If there is any other ways for simpler and better nomenclature method that could reduce confusion and make the MAP kinases terminology easier and straightforward, it may be time to adopt it.
Notes
References
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