Lipids get new comprehensive classification system

In response to the growing number of lipids expected to be discovered through lipidomics and in anticipation of the massive amounts of data that will be generated by the lipid community, an international group of scientists has developed a comprehensive classification, nomenclature, and chemical representation system for lipids. The details of the system appear in the May issue of the Journal of Lipid Research, an American Society for Biochemistry and Molecular Biology journal.

The new system is part of an effort by the Lipid Metabolites and Pathways Strategy (LIPID MAPS) consortium to produce a detailed understanding of the structure and function of all the lipids within a cell. The consortium is a large collaborative effort led by the University of California, San Diego and funded by a $35 million "Glue Grant" from the National Institute of General Medical Sciences. The five-year grant involves more than 30 researchers at 18 universities, medical research institutes, and companies across the United States.

The Director of the LIPID MAPS initiative and senior author of the manuscript Dr. Edward A. Dennis, Distinguished Professor of Chemistry, Biochemistry, and Pharmacology at the University of California, San Diego says: "The goals of the LIPID MAPS initiative are to characterize known lipids and identify new ones, to quantitate the temporal and spatial changes in lipids that occur with cellular metabolism, and to develop bioinformatics approaches that establish dynamic lipid networks. In order to coordinate their efforts with those of other groups, such as the Lipid Bank in Japan, the European Lipidomics Initiative, and the International Conference on the Biochemistry of Lipids based in Europe and to facilitate international collaboration, LIPID MAPS initiated the development of a comprehensive classification system for lipids suitable for databasing."

"The classification scheme was designed to be a broad-based scheme covering eukaryotic and prokaryotic sources, to include new classes of lipids which have been discovered in recent years, to be extensible to accommodate future novel classes and to be compatible with modern-day informatics requirements," explains the paper's first author Dr. Eoin Fahy, of the San Diego Supercomputer Center at the University of California, San Diego, who serves as LIPID MAPS' Bioinformatics Project Coordinator.

In the LIPID MAPS classification scheme, lipids are divided into eight primary categories: fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, prenol lipids, saccharolipids, and polyketides. These categories are based on the functional backbone of the lipid molecule from a chemical standpoint. The categories are further subdivided into classes and subclasses to handle the existing and emerging arrays of lipid structures.

In conjunction with their proposed lipid classification scheme, the group has also proposed a nomenclature system. "The nomenclature rules adopted by LIPID MAPS follow existing IUPAC-IUBMB rules closely and should not be viewed as a competing format," emphasizes Dr. Fahy. "The main differences involve clarification of the use of core structures to simplify systematic naming of some of the more complex lipids, provision of systematic names for recently discovered lipid classes, and clarification of abbreviations and shorthand names for lipids."

LIPID MAPS has also devised a common scheme for representing the chemical structures of individual lipids and their derivatives. The concept underlying the new methodology is that head groups are drawn on the right side and the hydrocarbon chain extends to the left. In the simplest case of the fatty acid derivatives, the acid group is drawn on the right and the hydrophobic hydrocarbon chain is on the left.

Another part of the classification system is a 12 digit identifier for each unique lipid molecule, called a LIPID ID. The identifier is based on the classification scheme and will be used mainly in databases, such as the LIPID MAPS database. "The format of the LIPID ID provides a systematic means of assigning unique IDs to lipid molecules and allows for the addition of large numbers of new categories, classes and subclasses in the future," explains Dr. Fahy. "The first two characters (1-2) of the ID contain the database identifier (e.g. LM for LIPID MAPS). The next two characters (3-4) correspond to the lipid category, the next two (5-6) to the class within that category and the next two (7-8) to the subclass. The last four characters of the ID comprise a unique identifier within a particular subclass and are randomly assigned."

The new classification system has already been implemented, and Dr. Dennis, Dr. Fahy and their collaborators from Europe, Asia, and across the U.S. hope that it will eventually gain widespread acceptance. "Inevitably, there will be some resistance, possibly from others who have created alternative schemes or who are long-time proponents of other formats," acknowledges Dr. Fahy. "However, the Journal of Lipid Research manuscript outlining this classification scheme contains an international panel of authors (several of whom are not involved with the LIPID MAPS project) and has also been reviewed by several other experts in the lipid research field, so it represents a well-balanced consensus view of what a modern-day lipid classification scheme should be."

Examples of the classification scheme and interactive access to it can be viewed on the LIPID MAPS website at http://www.lipidmaps.org.

Source : American Society for Biochemistry and Molecular Biology