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RNAi-based biosynthetic pathway screens to identify in vivo functions of non-nucleic-acid-based metabolites such as lipids #MMPMID25837419
Zhang H; Abraham N; Khan LA; Gobel V
Nat Protoc 2015[May]; 10 (5): 681-700 PMID25837419show ga
The field of metabolomics continues to catalog new compounds, but their functional analysis remains technically challenging, and roles beyond metabolism are largely unknown. Unbiased genetic/RNAi screens are powerful tools to identify the in vivo functions of protein-encoding genes, but not of non-proteinaceous compounds such as lipids. They can, however, identify the biosynthetic enzymes ? of these compounds- findings that are usually dismissed, as these typically synthesize multiple products. Here, we provide a method using follow-on biosynthetic-pathway screens to identify the endpoint biosynthetic enzyme and thus the compound through which they act. The approach is based on the principle that all subsequently identified downstream biosynthetic enzymes contribute to the synthesis of at least this one end product. We describe how to: systematically target lipid biosynthetic pathways; optimize targeting conditions; take advantage of pathway branchpoints; and validate results by genetic assays and biochemical analyses. This approach extends the power of unbiased genetic/RNAi screens to identify in vivo functions of non-nucleic-acid-based metabolites beyond their metabolic roles.