The immunity-related GTPases (IRGs) are a family of proteins induced by interferon-␥ that play a crucial role in innate resistance to intracellular pathogens. The M subfamily of IRG proteins (IRGM) plays a profound role in this context, in part because of the ability of its members to regulate the localization and expression of other IRG proteins. We present here evidence that IRGM proteins affect the localization of the guanylatebinding proteins (GBPs), a second family of interferon-induced GTP-binding proteins that also function in innate immunity. Absence of Irgm1 or Irgm3 led to accumulation of Gbp2 in intracellular compartments that were positive for both the macroautophagy (hereafter referred to as autophagy) marker LC3 and the autophagic adapter molecule p62/Sqstm1. Gbp2 was similarly relocalized in cells in which autophagy was impaired because of the absence of Atg5. Both in Atg5-and IRGM-deficient cells, the IRG protein Irga6 relocalized to the same compartments as Gbp2, raising the possibility of a common regulatory mechanism. However, other data indicated that Irga6, but not Gbp2, was ubiquitinated in IRGM-deficient cells. Similarly, coimmunoprecipitation studies indicated that although Irgm3 did interact directly with Irgb6, it did not interact with Gbp2. Collectively, these data suggest that IRGM proteins indirectly modulate the localization of GBPs through a distinct mechanism from that through which they regulate IRG protein localization. Further, these results suggest that a core function of IRGM proteins is to regulate autophagic flux, which influences the localization of GBPs and possibly other factors that instruct cell-autonomous immune resistance.The innate immune system is comprised of multiple effector pathways that are induced in host cells by proinflammatory cytokines such as IFN-␥. Such effectors confer on the host cells the ability to more easily eradicate invading pathogens through diverse mechanisms (1-4). A prominent family of IFN-␥-induced proteins that are required for resistance to intracellular bacteria and protozoa are the immunity-related GTPases. IRG 2 proteins share a number of biochemical functions: they are GTPases (5, 6), they bind lipid membranes in various intracellular membrane compartments (6 -8), and they form dimers and/or oligomers (5, 9). These and other characteristics relate them to the dynamins, a large family of GTPbinding proteins that are involved in vesicle formation, vesicle trafficking, and other aspects of lipid membrane remodeling (10 -12). Like the dynamins, current models suggest that the IRGs modulate membrane processing in cells (8, 13), which in turn impacts pathogen survival and/or leukocyte functioning.IRG proteins can be separated into the IRGA, IRGB, IRGC, IRGD, and IRGM subfamilies based on homology across the GTP-binding domain (14). Proteins in the IRGM subfamily are distinguished from the other proteins by possessing a non-canonical GMS sequence in the first GTP-binding motif (G1), whereas the remaining subfamilies all possess the canonical...