30 31 Mycobacterium tuberculosis, the etiologic agent of human tuberculosis, is the 32 world's leading cause of death from an infectious disease. One of the main 33 features of this pathogen is the complex and dynamic lipid composition of the cell 34 envelope, which adapts to the variable host environment and defines the fate of 35 infection by actively interacting with and modulating immune responses. Fine 36 regulation of de novo fatty acid biosynthesis, and its interaction with other 37 peripheral lipid pathways, is essential for cell membrane homeostasis while quickly 38 adapting to the growth environment. However, while much has been learned about 39 the enzymes of the numerous lipid pathways present in M. tuberculosis, little 40 knowledge is available regarding the proteins and metabolic signals regulating lipid 41 metabolism during infection. Previous studies on the regulation of lipid biosynthesis 42 in mycobacteria identified FasR as an essential transcriptional activator of de novo 43 fatty acid biosynthesis in Mycobacterium smegmatis. In this work, we constructed 44 and characterized a FasR-deficient mutant in M. tuberculosis and demonstrated 45 that FasR positively regulates fas and acpS expression. Lipidomic analysis of the 46 wild type and mutant strains revealed complete rearrangement of most lipid 47 components of the cell envelope, with phospholipids, mycolic acids, sulfolipids and 48 phthiocerol dimycocerosates relative abundance severely altered. As a 49 consequence, replication of the mutant strain was impaired in macrophages 50 leading to reduced virulence in a mouse model of infection. Moreover, we show 51 that the fasR mutant resides in acidified cellular compartments, suggesting that the 3 52 lipid perturbation caused by the mutation prevented M. tuberculosis inhibition of 53 phagolysosome maturation. This study identified FasR as a novel factor involved in 54 regulation of mycobacterial virulence and provides evidence for the essential role 55 that modulation of lipid homeostasis plays in the outcome of M. tuberculosis 56 infection. 57 58 Author summary 59 60 Tuberculosis is the leading cause of death from a single infectious disease, 61 resulting in approximately 1.5 million deaths per year worldwide. The composition 62 and complexity of the cell envelope is the most distinctive feature of 63 Mycobacterium tuberculosis, the etiologic agent of human tuberculosis. As the 64 mycobacterial cell envelope is the interface with the host, the modulation of its 65 structure and consequent responsiveness to immune factors might be important in 66 determining the state of an infection. We have previously identified FasR as an 67 essential transcriptional activator of de novo fatty acid biosynthesis in 68 Mycobacterium smegmatis. In this study, a M. tuberculosis mutant strain in fasR 69 was constructed and analyzed. Inactivation of fasR in M. tuberculosis was not 70 lethal for in vitro growth but led to rearrangement of the lipid composition of the cell 71 envelope. Consequently, the mutant strain w...