Protein post-translation modifications expand the chemical, molecular, and physiological diversity encoded by the genetic code. Types of protein modifications are numerous and diverse to suit wide functional roles. Lysine fatty acylation (KFA) is the covalent addition of long-chain fatty acyl groups to the lysine side chain amine. Despite being discovered over 30 years ago, relatively little is known about KFA. Recently, several mammalian enzymes were found to be able to efficiently remove KFA from proteins and multiple bacterial pathogens were discovered to mediate pathogenicity in part by catalyzing the addition of KFA. This thesis discusses findings that reveal KFA as a newly appreciated battleground during bacterial infection. V. cholerae, the causative agent of the disease cholera, secrets MARTX, a multi-domain toxin protein that contains a Rho-GTPase inactivating domain (RID). RID catalyzes KFA addition to RhoA family GTPases. We found that HDAC11 can hydrolyze lysine fatty acylation on RID to decrease it activity towards mammalian substrates. Bone marrow derived macrophages that lack HDAC11 phagocytose less V. cholerae. Correspondingly, mice lacking HDAC11 are defective in being able to clear a V. cholerae infection. We find that SIRT2 can promote defense of S. flexneri through KFA hydrolysis. IcsB is a KFA transferase from S. flexneri that promotes bacterial survival by inhibiting host autophagic machinery. S. flexneri also secretes IpaJ which causes Golgi stress. Golgi stress activates the transcription factor CREB3 to upregulate SIRT2. SIRT2 then hydrolyzes IcsB-catalyzed KFA to promote bacterial elimination. Mice that lack SIRT2 are more susceptible to S. flexneri infection. We also identify three novel KFA transferase toxins from L. pnuemophila, the pathogen that causes a pneumonia known as Legionnaire’s disease. We go on to identify the substrates of the most active toxin, lpg1387, and establish that the endogenous lpg1387 modulates KFA during L. pmuemophila infection.