Research Article: Natural variation in the roles of C. elegans autophagy components during microsporidia infection

Date Published: April 23, 2019

Publisher: Public Library of Science

Author(s): Keir M. Balla, Vladimir Lažetić, Emily R. Troemel, Read Pukkila-Worley.


Natural genetic variation can determine the outcome of an infection, and often reflects the co-evolutionary battle between hosts and pathogens. We previously found that a natural variant of the nematode Caenorhabditis elegans from Hawaii (HW) has increased resistance against natural microsporidian pathogens in the Nematocida genus, when compared to the standard laboratory strain of N2. In particular, HW animals can clear infection, while N2 animals cannot. In addition, HW animals have lower levels of initial colonization of Nematocida inside intestinal cells, compared to N2. Here we investigate how this natural variation in resistance relates to autophagy. We found that there is much better targeting of autophagy-related machinery to parasites under conditions where they are cleared. In particular, ubiquitin targeting to Nematocida cells correlates very well with their subsequent clearance in terms of timing, host strain and age, as well as species of Nematocida. Furthermore, clearance correlates with targeting of the LGG-2/LC3 autophagy protein to parasite cells, with HW animals having much more efficient targeting of LGG-2 to parasite cells than N2 animals. Surprisingly, however, we found that LGG-2 is not required to clear infection. Instead, we found that LGG-2/LC3 regulates Nematocida colonization inside intestinal cells. Interestingly, LGG-2/LC3 regulates intracellular colonization only in the HW strain, and not in N2. Altogether these results demonstrate that there is natural genetic variation in an LGG-2-dependent process that regulates microsporidia colonization inside intestinal cells, although not microsporidia clearance.

Partial Text

Natural genetic variation underlies differences in susceptibility to infection and inflammation among individuals [1]. Genome-wide association studies in humans have revealed genetic variation in innate immune genes that predispose individuals to increased risk of infection and autoimmune disease. For example, polymorphisms in autophagy genes Nod2, ATG16L, and IRGM are associated with increased risk for Crohn’s disease, which is an inflammatory bowel disease characterized by a dysregulated gut microbiome [2, 3]. The discovery that natural variation in autophagy genes can lead to differences in inflammation is part of a large body of evidence indicating a close connection between inflammation, intestinal immunity, and autophagy [4–6].

These studies reveal natural variation in the roles of C. elegans autophagy-related machinery in response to natural Nematocida pathogens (Fig 6). We observe natural variation in localization of ubiquitin to parasite cells in different strains, and this localization correlates very well with clearance of parasite. In addition, there is a correlation between clearance and localization of the autophagy protein LGG-2/LC3 to N. ironsii cells, with HW animals having increased targeting compared to N2 animals. These findings led us to hypothesize that parasite cells associated with LGG-2/LC3 are cleared, which could explain the greater resistance of HW animals compared to N2. However, we found that HW lgg-2 mutants can still clear infection, which does not support this hypothesis. Instead, we found that lgg-2 regulates the level of microsporidia colonization inside intestinal cells in HW animals, but not in N2 animals. The LGG-2 predicted amino acid sequence does not vary between N2 and HW (see Materials and methods). Furthermore, quantitative genetic studies indicate that the basis for the N2 and HW difference maps to chromosomes II, III and V, and not to chromosome IV, where lgg-2 resides [28]. Therefore, we do not favor a hypothesis that lgg-2 itself is responsible for the genetic variation between these two strains. Instead, we propose that an lgg-2-dependent process (and not lgg-2 itself) is active in HW animals to regulate levels of colonization, and is not active in N2 animals. In addition, our findings indicate that an lgg-2-independent process mediates clearance.