Systematic Screening for Novel Lipids by Shotgun Lipidomics

Abstract

A commonly accepted LIPID MAPS classification recognizes eight major lipid categories and over 550 classes, while new lipid classes are still being discovered by targeted biochemical approaches. Despite their compositional diversity, complex lipids such as glycerolipids, glycerophospholipids, saccharolipids, etc. are constructed from unique structural moieties, e.g., glycerol, fatty acids, choline, phosphate, and trehalose, that are linked by amide, ether, ester, or glycosidic bonds. This modular organization is also reflected in their MS/MS fragmentation pathways, such that common building blocks in different lipid classes tend to generate common fragments. We take advantage of this stereotyped fragmentation to systematically screen for new lipids sharing distant structural similarity to known lipid classes and have developed a discovery approach based on the computational querying of shotgun mass spectra by LipidXplorer software. We applied this concept for screening lipid extracts of C. elegans larvae at the dauer and L3 stages that represent alternative developmental programs executed in response to environmental challenges. The search, covering more than 1.5 million putative chemical compositions, identified a novel class of lyso-maradolipids specifically enriched in dauer larvae.

The Caenorhabditis elegans lipidome

“…Analysis revealed a novel class of lipids called lyso-maradolipids having only one fatty acid moiety specifically enriched in dauer larvae. Furthermore relative abundances of fatty acid side chains could be calculated for marado and lyso-maradolipids [95]. Due to missing chromatography direct infusion experiments benefit from employing high-resolution instrumentation.…”

RNAi-based biosynthetic pathway screens to identify in vivo functions of non-nucleic acid–based metabolites such as lipids

“…We demonstrate the approach with lipids, specifically, membrane lipids, and illustrate it with our prior RNAi feeding screen on epithelial polarity in C. elegans (see refs. 10–17 and http://www.wormbase.org for the expanding field of lipid biology and metabolomics in C. elegans ). The concept of the approach should, however, be equally effective in other genetic model organisms (limited only by their accessibility to specific targeting procedures), and it should serve to identify the functions of other categories of lipids or other non-template-derived compounds, such as, for instance, sugars.…”

LipidFrag: Improving reliability of in silico fragmentation of lipids and application to the Caenorhabditis elegans lipidome

“…Several lipid classes are present in the worm and different fatty acid combinations, including odd-numbered side chains, are possible in glycerol- and glycerophospholipids. Shotgun lipidomics was applied for analysis of a novel class of lipids only present in dauer larvae [31]. …”