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 lipidmaps.


The American Society for Biochemistry and Molecular Biology (ASBMB) is a nonprofit scientific and educational organization
with over 11,000 members in the United States and internationally. Most members teach and conduct research at colleges and
universities. Others conduct research in various government laboratories, nonprofit research institutions, and industry.



Founded in 1906, the Society is based in Bethesda, Maryland, on the campus of the Federation of American Societies for
Experimental Biology. The Society's primary purpose is to advance the sciences of biochemistry and molecular biology through
its publications, the Journal of Biological Chemistry, the Journal of Lipid Research, Molecular and Cellular Proteomics, and
Biochemistry and Molecular Biology Education, and the holding of scientific meetings.


For more information about ASBMB, see the Society's website at asbmb.


Contact: Nicole Kresge

nkresgeasbmb

301-634-7415

American Society for Biochemistry and Molecular Biology

asbmb.