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1. Multiple pals gene modules control a balance between immunity and development in Caenorhabditis elegans

   https://doi.org/10.1371/journal.ppat.1011120  

   Lažetić, Vladimir; Blanchard, Michael J.; Bui, Theresa; Troemel, Emily R. (July 2023, PLOS Pathogens)

   Schneider, David S. (Ed.)

   The immune system continually battles against pathogen-induced pressures, which often leads to the evolutionary expansion of immune gene families in a species-specific manner. For example, thepalsgene family expanded to 39 members in theCaenorhabditis elegansgenome, in comparison to a single mammalianpalsortholog. Our previous studies have revealed that two members of this family,pals-22andpals-25, act as antagonistic paralogs to control the Intracellular Pathogen Response (IPR). The IPR is a protective transcriptional response, which is activated upon infection by two molecularly distinct natural intracellular pathogens ofC.elegans–the Orsay virus and the fungusNematocida parisiifrom the microsporidia phylum. In this study, we identify a previously uncharacterized member of thepalsfamily,pals-17, as a newly described negative regulator of the IPR.pals-17mutants show constitutive upregulation of IPR gene expression, increased immunity against intracellular pathogens, as well as impaired development and reproduction. We also find that two other previously uncharacterizedpalsgenes,pals-20andpals-16, are positive regulators of the IPR, acting downstream ofpals-17. These positive regulators reverse the effects caused by the loss ofpals-17on IPR gene expression, immunity, and development. We show that the negative IPR regulator protein PALS-17 and the positive IPR regulator protein PALS-20 colocalize inside and at the apical side of intestinal epithelial cells, which are the sites of infection for IPR-inducing pathogens. In summary, our study demonstrates that severalpalsgenes from the expandedpalsgene family act as ON/OFF switch modules to regulate a balance between organismal development and immunity against natural intracellular pathogens inC.elegans. 

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2. Proteasome inhibition triggers tissue-specific immune responses against different pathogens in C. elegans

   https://doi.org/10.1371/journal.pbio.3002543  

   Grover, Manish; Gang, Spencer S; Troemel, Emily R; Barkoulas, Michalis (March 2024, PLOS Biology)

   Simon, Hans-Uwe (Ed.)

   Protein quality control pathways play important roles in resistance against pathogen infection. For example, the conserved transcription factor SKN-1/NRF up-regulates proteostasis capacity after blockade of the proteasome and also promotes resistance against bacterial infection in the nematodeCaenorhabditis elegans. SKN-1/NRF has 3 isoforms, and the SKN-1A/NRF1 isoform, in particular, regulates proteasomal gene expression upon proteasome dysfunction as part of a conserved bounce-back response. We report here that, in contrast to the previously reported role of SKN-1 in promoting resistance against bacterial infection, loss-of-function mutants inskn-1aand its activating enzymesddi-1andpng-1show constitutive expression of immune response programs against natural eukaryotic pathogens ofC.elegans. These programs are the oomycete recognition response (ORR), which promotes resistance against oomycetes that infect through the epidermis, and the intracellular pathogen response (IPR), which promotes resistance against intestine-infecting microsporidia. Consequently,skn-1amutants show increased resistance to both oomycete and microsporidia infections. We also report that almost all ORR/IPR genes induced in common between these programs are regulated by the proteasome and interestingly, specific ORR/IPR genes can be induced in distinct tissues depending on the exact trigger. Furthermore, we show that increasing proteasome function significantly reduces oomycete-mediated induction of multiple ORR markers. Altogether, our findings demonstrate that proteasome regulation keeps innate immune responses in check in a tissue-specific manner against natural eukaryotic pathogens of theC.elegansepidermis and intestine. 

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3. Novel infection by Mucor hiemalis kills Caenorhabditis hosts through intestinal perforation

   https://doi.org/10.1128/iai.00310-25  

   Ni, Jay; Weigand, Spencer; Sowa, Jessica N (May 2026, Infection and Immunity)

   The nematode Caenorhabditis elegans has emerged as a popular model system to investigate cell biology and host-pathogen interactions. Presently, C. elegans is studied as a natural host of intracellular pathogens such as microsporidia and Orsay virus, along with extracellular bacterial and fungal pathogens. The use of C. elegans as a model in host-pathogen research is limited by the number of naturally occurring pathogens that infect this organism. Through a sampling project to identify new pathogens of C. elegans, we identified the fungus Mucor hiemalis as a pathogen of Caenorhabditis species. We observed the fungus in the intestinal lumen of wild-caught Caenorhabditis briggsae, and co-culturing the wild-caught species with infection reporter C. elegans confirmed infection by M. hiemalis. This study characterizes the fungal infection by M. hiemalis in Caenorhabditis nematodes. Fluorescence microscopy with fungal staining revealed the life cycle of M. hiemalis within multiple Caenorhabditis species at varying growth stages. We observed the killing of nematodes by M. hiemalis via intestinal perforation and assessed its host range through a series of lifespan assays. We investigated the food preference of C. elegans and determined that nematodes show a preference toward food that contain M. hiemalis sporangiospores. Last, we evaluated common C. elegans transcriptional immune responses and found that M. hiemalis induces the expression of genes related to the intracellular pathogen response. Characterization of this fungal infection in Caenorhabditis nematodes will provide new insights into the biology of pathogenic fungi and host immune responses. 

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4. Genomic and phenotypic evolution of nematode-infecting microsporidia

   https://doi.org/10.1371/journal.ppat.1011510  

   Wadi, Lina; El Jarkass, Hala Tamim; Tran, Tuan D.; Islah, Nizar; Luallen, Robert J.; Reinke, Aaron W. (July 2023, PLOS Pathogens)

   Grigg, Michael E. (Ed.)

   Microsporidia are a large phylum of intracellular parasites that can infect most types of animals. Species in theNematocidagenus can infect nematodes includingCaenorhabditis elegans, which has become an important model to study mechanisms of microsporidia infection. To understand the genomic properties and evolution of nematode-infecting microsporidia, we sequenced the genomes of nine species of microsporidia, including two genera,EnteropsectraandPancytospora, without any previously sequenced genomes. Core cellular processes, including metabolic pathways, are mostly conserved across genera of nematode-infecting microsporidia. Each species encodes unique proteins belonging to large gene families that are likely used to interact with host cells. Most strikingly, we observed one such family, NemLGF1, is present in bothNematocidaandPancytosporaspecies, but not any other microsporidia. To understand howNematocidaphenotypic traits evolved, we measured the host range, tissue specificity, spore size, and polar tube length of several species in the genus. Our phylogenetic analysis shows thatNematocidais composed of two groups of species with distinct traits and that species with longer polar tubes infect multiple tissues. Together, our work details both genomic and trait evolution between related microsporidia species and provides a useful resource for further understanding microsporidia evolution and infection mechanisms. 

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5. A web application for gene-based queries of CaeNDR RNA-seq data

   https://doi.org/10.17912/micropub.biology.001194  

   Bell, Avery Davis; Paaby, Annalise B (January 2024, microPublication Biology)

   Variation in gene expression is a feature of all living systems and has recently been characterized extensively among wild strains of the model organism Caenorhabditis elegans. To enable researchers to query gene expression and gene expression variation at any gene of interest, we have created a user-friendly web application that shares RNA-seq transcription data for 208 wild C. elegans strains generated by the Caenorhabditis Natural Diversity Resource (CaeNDR). Here, we describe the features of the web application and the details of the data and data processing underlying it. We hope that this website, wildworm.biosci.gatech.edu/cendrexp/, will help C. elegans researchers better understand their favorite genes and strains. 

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