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Mycobacterial fatty acid catabolism is repressed by FdmR to sustain lipogenesis and virulence

Significance An improved understanding of fatty acid metabolism in pathogenic mycobacteria is critical for development of new chemotherapeutics. Here, we identified FdmR, a previously uncharacterized transcriptional factor, as the key regulator of fatty acid catabolism in the pathogen Mycobacterium marinum. We demonstrated that FdmR optimizes fatty acid utilization and allows for a high rate of cell growth with modest consumption of the nutrients. Moreover, we found that FdmR suppresses degradation of de novo-synthesized fatty acids and controls the size and abundance of virulence-associated lipids and mycolates. These results reveal that FdmR-mediated regulation serves important functions in mycobacterial physiology and pathogenicity. Thus, this study identifies FdmR as a potentially attractive target for novel therapeutic intervention. Host-derived fatty acids are an important carbon source for pathogenic mycobacteria during infection. How mycobacterial cells regulate the catabolism of fatty acids to serve the pathogenicity, however, remains unknown. Here, we identified a TetR-family transcriptional factor, FdmR, as the key regulator of fatty acid catabolism in the pathogen Mycobacterium marinum by combining use of transcriptomics, chromatin immunoprecipitation followed by sequencing, dynamic 13C-based flux analysis, metabolomics, and lipidomics. An M. marinum mutant deficient in FdmR was severely attenuated in zebrafish larvae and adult zebrafish. The mutant showed defective growth but high substrate consumption on fatty acids. FdmR was identified as a long-chain acyl-coenzyme A (acyl-CoA)–responsive repressor of genes involved in fatty acid degradation and modification. We demonstrated that FdmR functions as a valve to direct the flux of exogenously derived fatty acids away from β-oxidation toward lipid biosynthesis, thereby avoiding the overactive catabolism and accumulation of biologically toxic intermediates. Moreover, we found that FdmR suppresses degradation of long-chain acyl-CoAs endogenously synthesized through the type I fatty acid synthase. By modulating the supply of long-chain acyl-CoAs for lipogenesis, FdmR controls the abundance and chain length of virulence-associated lipids and mycolates and plays an important role in the impermeability of the cell envelope. These results reveal that despite the fact that host-derived fatty acids are used as an important carbon source, overactive catabolism of fatty acids is detrimental to mycobacterial cell growth and pathogenicity. This study thus presents FdmR as a potentially attractive target for chemotherapy.