Isolation and Characterization of the Natural Microbiota of the Model Nematode <em>Caenorhabditis elegans</em>

The nematode Caenorhabditis elegans interacts with a large diversity of microorganisms in nature. In general, C. elegans is commonly found in rotten plant ...

University of Kiel

The invertebrate immune system comprises physiological mechanisms, physical barriers and also behavioral responses. It is generally related to the vertebrate innate immune system and widely believed to provide nonspecific defense against pathogens, whereby the response to different pathogen types is usually mediated by distinct signalling cascades. Recent work suggests that invertebrate immune defense can be more specific at least at the phenotypic level. The underlying genetic mechanisms are as yet poorly understood.

Contrasting invertebrate immune defense behaviors caused by a single gene, the Caenorhabditis elegans neuropeptide receptor gene npr-1.

Nematodes and arthropods likely form the taxon Ecdysozoa. Information on antimicrobial effectors from the model nematode Caenorhabditis elegans may thus shed light on the evolutionary origin of these defences in arthropods. This nematode species possesses an extensive armory of putative antimicrobial effector proteins, such as lysozymes, caenopores (or saposin-like proteins), defensin-like peptides, caenacins and neuropeptide-like proteins, in addition to the production of reactive oxygen species and autophagy. As C. elegans is a bacterivore that lives in microbe-rich environments, some of its effector peptides and proteins likely function in both digestion of bacterial food and pathogen elimination. In this review, we provide an overview of C. elegans immune effector proteins and mechanisms. We summarize the experimental evidence of their antimicrobial function and involvement in the response to pathogen infection. We further evaluate the microbe-induced expression of effector genes using WormExp, a recently established database for C. elegans gene expression analysis. We emphasize the need for further analysis at the protein level to demonstrate an antimicrobial activity of these molecules both in vitro and in vivoThis article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'.

Antimicrobial effectors in the nematode Caenorhabditis elegans: an outgroup to the Arthropoda.

Invertebrate defence against pathogens exclusively relies on components of the innate immune system. Comprehensive information has been collected over the last years on the molecular components of invertebrate immunity and the involved signalling processes, especially for the main invertebrate model species, the fruitfly Drosophila melanogaster and the nematode Caenorhabditis elegans. Yet, the exact regulation of general and specific defences is still not well understood. In the current study, we take advantage of a recently established database, WormExp, which combines all available gene expression studies for C. elegans, in order to explore commonalities and differences in the regulation of nematode immune defence against a large variety of pathogens versus food microbes. We identified significant overlaps in the transcriptional response towards microbes, especially pathogenic bacteria. We also found that the GATA motif is overrepresented in many microbe-induced gene sets and in targets of other previously identified regulators of worm immunity. Moreover, the activated targets of one of the known C. elegans GATA transcription factors, ELT-2, are significantly enriched in the gene sets, which are differentially regulated by gut-infecting pathogens. These findings strongly suggest that GATA transcription factors and particularly ELT-2 play a central role in regulating the C. elegans immune response against gut pathogens. More specific responses to distinct pathogens may be mediated by additional transcription factors, either acting alone or jointly with GATA transcription factors. Taken together, our analysis of the worm's transcriptional response to microbes provides a new perspective on the C. elegans immune system, which we propose to be coordinated by GATA transcription factor ELT-2 in the gut.

GATA transcription factor as a likely key regulator of the Caenorhabditis elegans innate immune response against gut pathogens.

C-type lectin-like domain (CTLD) proteins occupy crucial functions in the immune system of vertebrates, but their role in invertebrate immunity is much less understood. The nematode Caenorhabditis elegans possesses a highly diverse CTLD protein encoding (clec) gene repertoire. A role of C. elegans clec genes in pathogen defense is always assumed, yet experimental evidence for clec immune function is rare. To systematically test the potential function of clec genes in the C. elegans defense against pathogens, we screened 39 clec mutants for survival on the Gram-positive pathogen Bacillus thuringiensis (BT18247) and 37 clec mutants on the Gram-negative pathogen Pseudomonas aeruginosa (PA14). We found that clec mutants can exhibit either decreased or, unexpectedly, increased resistance to infection. Since we observed high escape behavior for some of the clec mutants on BT18247 during the initial screen, we then asked if increased pathogen avoidance behavior underlies the increased resistance of some clec mutants. We thus tested lawn leaving behavior of the resistant clec-29(ok3181), clec-34(ok2120), clec-151(ok2264), and C54G4.4(ok2110) mutant on BT18247. We found that C54G4.4(ok2110) mutant animals exhibit a particularly strong lawn leaving behavior, in addition to prolonged feeding cessation when exposed to BT18247. Together, our results indicate that clec genes mediate both resistance and susceptibility to infection. Further, behavioral analyses of the C54G4.4(ok2110) mutant implicate C54G4.4 in the regulation of pathogen avoidance behavior towards BT18247. We conclude that C. elegans clec genes may act both as positive and negative regulators of physiological as well as behavioral immune defense responses.

Enhanced behavioral immune defenses in a C. elegans C-type lectin-like domain gene mutant.

Caenorhabditis elegans is associated in nature with a species-rich, distinct microbiota, which was characterized only recently [1]. Thus, our understanding of the relevance of the microbiota for nematode fitness is still at its infancy. One major benefit that the intestinal microbiota can provide to its host is protection against pathogen infection [2]. However, the specific strains conferring the protection and the underlying mechanisms of microbiota-mediated protection are often unclear [3]. Here, we identify natural C. elegans microbiota isolates that increase C. elegans resistance to pathogen infection. We show that isolates of the Pseudomonas fluorescens subgroup provide paramount protection from infection with the natural pathogen Bacillus thuringiensis through distinct mechanisms. We found that the P. lurida isolates MYb11 and MYb12 (members of the P. fluorescens subgroup) protect C. elegans against B. thuringiensis infection by directly inhibiting growth of the pathogen both in vitro and in vivo. Using genomic and biochemical analyses, we further demonstrate that MYb11 and MYb12 produce massetolide E, a cyclic lipopeptide biosurfactant of the viscosin group [4, 5], which is active against pathogenic B. thuringiensis. In contrast to MYb11 and MYb12, P. fluorescens MYb115-mediated protection involves increased resistance without inhibition of pathogen growth and most likely depends on indirect, host-mediated mechanisms. This work provides new insight into the functional significance of the C. elegans natural microbiota and expands our knowledge of bacteria-derived compounds that can influence pathogen colonization in the intestine of an animal.

Natural C. elegans Microbiota Protects against Infection via Production of a Cyclic Lipopeptide of the Viscosin Group.

microRNAs (miRNAs) are small non-coding RNA-molecules that influence translation by binding to the target gene mRNA. Many miRNAs are found in nested arrangements within larger protein-coding host genes. miRNAs and host genes in a nested arrangement are often transcribed simultaneously, which may indicate that both have similar functions. miRNAs have been implicated in regulating defense responses against pathogen infection in C. elegans and in mammals. Here, we asked if miRNAs in nested arrangements and their host genes are involved in the C. elegans response against infection with Bacillus thuringiensis (Bt). We performed miRNA sequencing and subsequently focused on four nested miRNA-host gene arrangements for a functional genetic analysis. We identified mir-58.1 and mir-2 as negative regulators of C. elegans resistance to Bt infection. However, we did not find any miRNA/host gene pair in which both contribute to defense against Bt.

The effects of nested miRNAs and their host genes on immune defense against Bacillus thuringiensis infection in Caenorhabditis elegans.

Cells can detect pathogens through guard proteins that sense disturbances in core cellular processes, but the exact mechanisms often remain elusive. In this issue of Immunity, Orzalli et al. identify Bcl-2 family members as guard proteins that detect virus-induced translational inhibition and induce pyroptosis in human keratinocytes.

Guard proteins keep watch at epithelial walls.

The  natural microbiota was described only recently. Thus, our understanding of its effects on nematode physiology is still in its infancy. We previously showed that the  natural microbiota isolates  MYb11 and  MYb115 protect the worm against pathogens such as  (Bt). However, the overall effects of the protective microbiota on worm physiology are incompletely understood. Here, we investigated how MYb11 and MYb115 affect  lifespan, fertility, and intestinal colonization. We further studied the capacity of MYb11 and MYb115 to protect the worm against purified Bt toxins. We show that while MYb115 and MYb11 affect reproductive timing and increase early reproduction only MYb11 reduces worm lifespan. Moreover, MYb11 aggravates killing upon toxin exposure. We conclude that MYb11 has a pathogenic potential in some contexts. This work thus highlights that certain  microbiota members can be beneficial and costly to the host in a context-dependent manner, blurring the line between good and bad.

Katja Dierking

Evolutionary Ecology and Genetics

University of Kiel

Isolation and Characterization of the Natural Microbiota of the Model Nematode Caenorhabditis elegans

Katja Dierking

.css-o250i3{font-size:18px;font-family:Open Sans,sans-serif;line-height:21.6px;}Evolutionary Ecology and Genetics

University of Kiel

Isolation and Characterization of the Natural Microbiota of the Model Nematode Caenorhabditis elegans

Evolutionary Ecology and Genetics