Grant: Discovery Grants Program - Individual

Several commensal and parasitic microbes grow inside plant and animal cells. The goal of my research program is to elucidate the mechanisms by which they access and adapt to their ecological niche. We seek to advance knowledge of microbiology and host immunity that could be used to optimize the behavior of beneficial bacteria, and to prevent and treat infectious diseases of importance to the agricultural, food, biotechnology, and pharmaceutical sectors. Our models are clones of Escherichia coli, called Shigella species, whose pathogenesis relies on a type III secretion system (T3SS). The tractability of Shigella makes it a reference model for bacteria with a T3SS or a comparable lifestyle, broadening potential applications. The role of the T3SS during Shigella infection is to induce invasion of the cytoplasm of human intestinal cells, particularly macrophages and epithelial cells. To do this, the T3SS forces the host cell membrane to engulf Shigella, resulting in the formation of a Shigella-containing vacuole within the cytoplasm. The interaction of the vacuole with the endolysosomal compartment exposes Shigella to harsh conditions, including acidic pH. Finally, Shigella ruptures the vacuole to gain access to its replicative niche in the cytoplasm. In the past, this key step was difficult to study due to a lack of tools. Therefore, over the last decade we have developed a series of reporter systems that measure the activity of the T3SS while tracking the vacuolar and cytoplasmic subpopulations. In this next phase, we will use this expertise to study the adaptation mechanisms of Shigella during this vacuole-to-cytoplasm transition. To do this, we will use an approach that enriches for cytoplasmic or vacuolar subpopulations and study their gene expression at the genomic level during infection of intestinal epithelial cells. This will allow us to identify genes that are specifically activated in each compartment and test their implication in pathogenesis. Second, we will use a gene candidate approach to investigate a novel link we have identified between the T3SS and acid resistance genes that may provide Shigella with the ability to adapt to the low pH in the vacuole. Third, we will investigate how the rupture of the Shigella-containing vacuole in the specific context of macrophages may promote lysoptosis, a novel form of programmed cell death induced by endolysosomal proteases. Taken together, these studies will significantly advance our understanding of Shigella's adaptation to intracellular life, particularly during the transition from the vacuole to its replicative niche in the cytoplasm. We will explore the potential of the key processes identified as targets for the development of unconventional anti-infective strategies that could be used instead of antibiotics. These are critical applications for our world where the steady rise of antibiotic resistance poses a growing threat to the environment, food production and health systems.