Natural variants in C. elegans atg-5 3’UTR uncover divergent effects of autophagy on polyglutamine aggregation in different tissues

AbstractDiseases caused by protein misfolding and aggregation, in addition to cell selectivity, often exhibit variation among individuals in the age of onset, progression, and severity of disease. Genetic variation has been shown to contribute to such clinical variation. We have previously found that protein aggregation-related phenotypes in a model organism, C. elegans, can be modified by destabilizing polymorphisms in the genetic background and by natural genetic variation. Here, we identified a large modifier locus in a Californian wild strain of C. elegans, DR1350, that alters the susceptibility of the head muscle cells to polyglutamine (polyQ) aggregation, and causes an increase in overall aggregation, without changing the basal activity of the muscle proteostasis pathways known to affect polyQ aggregation. We found that the two phenotypes were genetically separable, and identified regulatory variants in a gene encoding a conserved autophagy protein ATG-5 (ATG5 in humans) as being responsible for the overall increase in aggregation. The atg-5 gene conferred a dosage-dependent enhancement of polyQ aggregation, with DR1350-derived atg-5 allele behaving as a hypermorph. Examination of autophagy in animals bearing the modifier locus indicated enhanced response to an autophagy-activating treatment. Because autophagy is known to be required for the clearance of polyQ aggregates, this result was surprising. Thus, we tested whether directly activating autophagy, either pharmacologically or genetically, affected the polyQ aggregation in our model. Strikingly, we found that the effect of autophagy on polyQ aggregation was tissue-dependent, such that activation of autophagy decreased polyQ aggregation in the intestine, but increased it in the muscle cells. Our data show that cryptic genetic variants in genes encoding proteostasis components, although not causing visible phenotypes under normal conditions, can have profound effects on the behavior of aggregation-prone proteins, and suggest that activation of autophagy may have divergent effects on the clearance of such proteins in different cell types.

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The ancestral C. elegans cuticle suppresses rol-1

10.1101/2020.02.07.938696 ◽

2020 ◽

Author(s):

Luke M. Noble ◽

Asif Miah ◽

Taniya Kaur ◽

Matthew V. Rockman

Keyword(s):

Genetic Variation ◽

Caenorhabditis Elegans ◽

Comparative Genomics ◽

Linkage Mapping ◽

Genetic Background ◽

Gene Editing ◽

Wild Strain ◽

Collagen Gene ◽

Natural Genetic Variation ◽

C Elegans

ABSTRACTGenetic background commonly modifies the effects of mutations. We discovered that worms mutant for the canonical rol-1 gene, identified by Brenner in 1974, do not roll in the genetic background of the wild strain CB4856. Using linkage mapping, association analysis and gene editing, we determined that N2 carries an insertion in the collagen gene col-182 that acts as a recessive enhancer of rol-1 rolling. From population and comparative genomics, we infer the insertion is derived in N2 and related laboratory lines, likely arising during the domestication of Caenorhabditis elegans, and breaking a conserved protein. The ancestral version of col-182 also modifies the phenotypes of four other classical cuticle mutant alleles, and the effects of natural genetic variation on worm shape and locomotion. These results underscore the importance of genetic background and the serendipity of Brenner’s choice of strain.

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Unexpected cell type-dependent effects of autophagy on polyglutamine aggregation revealed by natural genetic variation in C. elegans

BMC Biology ◽

10.1186/s12915-020-0750-5 ◽

2020 ◽

Vol 18 (1) ◽

Cited By ~ 2

Author(s):

J. Alexander-Floyd ◽

S. Haroon ◽

M. Ying ◽

A. A. Entezari ◽

C. Jaeger ◽

...

Keyword(s):

Genetic Variation ◽

Cell Type ◽

Natural Genetic Variation ◽

C Elegans ◽

Polyglutamine Aggregation

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Punctuated loci on chromosome IV determine natural variation in Orsay virus susceptibility of Caenorhabditis elegans strains Bristol N2 and Hawaiian CB4856

Journal of Virology ◽

10.1128/jvi.02430-20 ◽

2021 ◽

Author(s):

Mark G. Sterken ◽

Lisa van Sluijs ◽

Yiru A. Wang ◽

Wannisa Ritmahan ◽

Mitra L. Gultom ◽

...

Keyword(s):

Genetic Variation ◽

Caenorhabditis Elegans ◽

Virus Infection ◽

Genetic Architecture ◽

Recombinant Inbred Lines ◽

Model Organism ◽

C Elegans ◽

Viral Susceptibility ◽

Orsay Virus ◽

Insight Into

Host-pathogen interactions play a major role in evolutionary selection and shape natural genetic variation. The genetically distinct Caenorhabditis elegans strains, Bristol N2 and Hawaiian CB4856, are differentially susceptible to the Orsay virus (OrV). Here we report the dissection of the genetic architecture of susceptibility to OrV infection. We compare OrV infection in the relatively resistant wild-type CB4856 strain to the more susceptible canonical N2 strain. To gain insight into the genetic architecture of viral susceptibility, 52 fully sequenced recombinant inbred lines (CB4856 x N2 RILs) were exposed to OrV. This led to the identification of two loci on chromosome IV associated with OrV resistance. To verify the two loci and gain additional insight into the genetic architecture controlling virus infection, introgression lines (ILs) that together cover chromosome IV, were exposed to OrV. Of the 27 ILs used, 17 had an CB4856 introgression in an N2 background and 10 had an N2 introgression in a CB4856 background. Infection of the ILs confirmed and fine-mapped the locus underlying variation in OrV susceptibility and we found that a single nucleotide polymorphism in cul-6 may contribute to the difference in OrV susceptibility between N2 and CB4856. An allele swap experiment showed the strain CB4856 became as susceptible as the N2 strain by having an N2 cul-6 allele, although having the CB4856 cul-6 allele did not increase resistance in N2. Additionally, we found that multiple strains with non-overlapping introgressions showed a distinct infection phenotype from the parental strain, indicating that there are punctuated locations on chromosome IV determining OrV susceptibility. Thus, our findings reveal the genetic complexity of OrV susceptibility in C. elegans and suggest that viral susceptibility is governed by multiple genes. Importance Genetic variation determines the viral susceptibility of hosts. Yet, pinpointing which genetic variants determine viral susceptibility remains challenging. Here, we have exploited the genetic tractability of the model organism C. elegans to dissect the genetic architecture of Orsay virus infection. Our results provide novel insight into natural determinants of Orsay virus infection.

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Natural Genetic Variation in a Multigenerational Phenotype in C. elegans

Current Biology ◽

10.1016/j.cub.2018.05.091 ◽

2018 ◽

Vol 28 (16) ◽

pp. 2588-2596.e8 ◽

Cited By ~ 14

Author(s):

Lise Frézal ◽

Emilie Demoinet ◽

Christian Braendle ◽

Eric Miska ◽

Marie-Anne Félix

Keyword(s):

Genetic Variation ◽

Natural Genetic Variation ◽

C Elegans

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Natural genetic variation drives microbiome selection in the Caenorhabditis elegans gut

10.1101/2021.03.12.435148 ◽

2021 ◽

Author(s):

Fan Zhang ◽

Jessica L. Weckhorst ◽

Adrien Assié ◽

Ciara Hosea ◽

Christopher A. Ayoub ◽

...

Keyword(s):

Genetic Variation ◽

Caenorhabditis Elegans ◽

Signaling Pathways ◽

Insulin Signaling ◽

Natural Genetic Variation ◽

Microbiome Composition ◽

C Elegans ◽

Free Living Nematode ◽

Wild Strains ◽

The Stability

Host genetic landscapes can shape microbiome assembly in the animal gut by contributing to the establishment of distinct physiological environments. However, the genetic determinants contributing to the stability and variation of these microbiome types remain largely undefined. Here, we use the free-living nematode Caenorhabditis elegans to identify natural genetic variation among wild strains of C. elegans strains that drives assembly of distinct microbiomes. To achieve this, we first established a diverse model microbiome that represents the phylogenetic and functional diversity naturally found in the C. elegans microbiome. Using this community, we show that C. elegans utilizes immune, xenobiotic and metabolic signaling pathways to favor the assembly of different microbiome types. Variations in these pathways were associated with the enrichment for specific commensals, including the Alphaproteobacteria Ochrobactrum. Using RNAi and mutant strains, we showed that host selection for Ochrobactrum is mediated specifically by host insulin signaling pathways. Ochrobactrum recruitment is blunted in the absence of daf-2/IGFR and requires the insulin signaling transcription factors daf-16/FOXO and pqm-1/SALL2. Further, the ability of C. elegans to enrich for Ochrobactrum is correlated positively with host outcomes, as animals that develop faster are larger and have higher gut Ochrobactrum colonization as adults. These results highlight a new role for the highly conserved insulin signaling pathways in the regulation of microbiome composition in C. elegans.

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

10.1101/418749 ◽

2018 ◽

Author(s):

Keir M. Balla ◽

Vladimir Lažetić ◽

Emily Troemel

Keyword(s):

Genetic Variation ◽

Caenorhabditis Elegans ◽

Natural Variation ◽

Early Stage ◽

Laboratory Strain ◽

Host Strain ◽

Standard Laboratory ◽

Natural Genetic Variation ◽

C Elegans ◽

Natural Variant

AbstractNatural 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 intracellular colonization of Nematocida 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 Nematocida species. 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 loss of lgg-2 leads to increased intracellular colonization in the HW background, although interestingly, it does not affect colonization in the N2 background. Altogether our results suggest that there is natural genetic variation in an lgg-2-dependent process that regulates intracellular levels of microsporidia at a very early stage of infection prior to clearance.

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Balancing selection of the Intracellular Pathogen Response in natural Caenorhabditis elegans populations

10.1101/579151 ◽

2019 ◽

Author(s):

Lisa van Sluijs ◽

Kobus J. Bosman ◽

Frederik Pankok ◽

Tatiana Blokhina ◽

Joost A. G. Riksen ◽

...

Keyword(s):

Genetic Variation ◽

Caenorhabditis Elegans ◽

Balancing Selection ◽

Model Organism ◽

Evolutionary Strategies ◽

Intracellular Pathogen ◽

C Elegans ◽

Pathogen Response ◽

Orsay Virus ◽

Selection Of

AbstractBackgroundGenetic variation in host populations may lead to differential viral susceptibilities. Here, we investigate the role of natural genetic variation present for an antiviral pathway, the Intracellular Pathogen Response (IPR), underlying susceptibility to Orsay virus in the model organism Caenorhabditis elegans. The IPR involves transcriptional activity of 80 genes including the pals-genes. The pals-genes form an expanded gene family which hints they could be shaped by an evolutionary selective pressure. Here we examine the genetic variation in the pals-family for traces of selection and explore the molecular and phenotypic effects of having distinct pals-gene alleles.ResultsGenetic analysis of 330 world-wide C. elegans strains reveals that genetic diversity within the IPR-related pals-genes can be categorized in a few haplotypes worldwide. Importantly, two key-IPR regulators, pals-22 and pals-25, are in a genomic region carrying signatures of balancing selection. Therefore, distinct pals-22/pals-25 alleles have been maintained in C. elegans populations over time, which suggests different evolutionary strategies exist in IPR regulation. We investigated the IPR by infecting two C. elegans strains that represent distinct pals-22/pals-25 haplotypes, N2 and CB4856, with Orsay virus to determine their susceptibility and transcriptional response to infection. Our data suggests that regulatory genetic variation underlies constant high activity of IPR genes in CB4856 which could determine the host transcriptional defense. We found that CB4856 shows initially lower viral susceptibility than N2. High basal IPR expression levels might help counteract viral infection directly, whereas N2-like strains that need to activate the IPR genes first may have a slower response. Nevertheless, most wild strains harbor N2-like alleles for the pals-genes.ConclusionsOur work provides evidence for balancing genetic selection of immunity genes in C. elegans and illustrated how this may shape the transcriptional defense against pathogens. The transcriptional and genetic data presented in this study therefore provide a novel perspective on the functional diversity that can develop within a main antiviral response in natural host populations.

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Optogenetic analysis of Ca++ transients in Caenorhabditis elegans muscle cells during forward and reverse locomotion

10.1101/2020.12.02.408088 ◽

2020 ◽

Author(s):

Jacob R. Manjarrez ◽

Magera Shaw ◽

Roger Mailler

Keyword(s):

Caenorhabditis Elegans ◽

Muscle Activation ◽

Cell Activity ◽

Model Organism ◽

Muscle Cells ◽

Phase Lag ◽

C Elegans ◽

Calcium Indicators ◽

Body Wall Muscles ◽

Genetically Encoded Calcium Indicators

ABSTRACTUnderstanding how an organism generates movement is an important step toward determining how a system of neurons produces behavior. With only 95 body wall muscles and 302 neurons, Caenorhabditis elegans is an attractive model organism to use in uncovering the connection between neural circuitry and movement. This study provides a comprehensive examination of the muscle cell activity used by C. elegans during both forward and reverse locomotion. By tracking freely moving worms that express genetically encoded calcium indicators in their muscle cells, we directly measure the patterns of activity that occur during movement. We then analyzed these patterns using a variety of signal processing and statistical techniques. Although our results agree with many previous findings, we also discovered there is significantly different mean Ca++ levels in many of the muscle cells during forward and reverse locomotion and, when considered independently, the dorsal and ventral muscle activation waves exhibit classical neuromechanical phase lag (NPL).

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Dynein-dynactin segregate meiotic chromosomes in C. elegans spermatocytes

Development ◽

10.1242/dev.197780 ◽

2021 ◽

Vol 148 (3) ◽

pp. dev197780

Author(s):

Daniel J. Barbosa ◽

Vanessa Teixeira ◽

Joana Duro ◽

Ana X. Carvalho ◽

Reto Gassmann

Keyword(s):

Protein Misfolding ◽

Meiotic Chromosome ◽

Spindle Assembly ◽

Cell Types ◽

Cytoplasmic Dynein ◽

Early Embryo ◽

Loss Of Function ◽

C Elegans ◽

Spindle Elongation

ABSTRACTThe microtubule motor cytoplasmic dynein 1 (dynein) and its essential activator dynactin have conserved roles in spindle assembly and positioning during female meiosis and mitosis, but their contribution to male meiosis remains poorly understood. Here, we characterize the G33S mutation in the C. elegans dynactin subunit DNC-1, which corresponds to G59S in human p150Glued that causes motor neuron disease. In spermatocytes, dnc-1(G33S) delays spindle assembly and penetrantly inhibits anaphase spindle elongation in meiosis I, which prevents the segregation of homologous chromosomes. By contrast, chromosomes segregate without errors in the early dnc-1(G33S) embryo. Deletion of the DNC-1 N-terminus shows that defective meiosis in dnc-1(G33S) spermatocytes is not due to the inability of DNC-1 to interact with microtubules. Instead, our results suggest that the DNC-1(G33S) protein, which is aggregation prone in vitro, is less stable in spermatocytes than the early embryo, resulting in different phenotypic severity in the two dividing tissues. Thus, the dnc-1(G33S) mutant reveals that dynein-dynactin drive meiotic chromosome segregation in spermatocytes and illustrates that the extent to which protein misfolding leads to loss of function can vary significantly between cell types.

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