Anderson, E. C. et al. (2019) International Worm Meeting "X-Chromosome Domain Achitecture Regulates Caenorhabditis elegans Lifespan but Not Dosage Compensation."

Dillin, A., Shin, A., Kenyon, C., Frankino, P. A., Bian, Q., Meyer, B. J., Yang, Q, Anderson, E. C., Podshivalova, K., Higuchi-Sanabria, R.

[International Worm Meeting, 2019]

Interphase chromosomes are organized into a series of structures ranging from kilobase-scale chromatin loops, to megabase-scale topologically associating domains (TADs), to territories comprising hundreds of megabases. Loci within a TAD interact predominantly with each other while being insulated from interactions with loci in neighboring TADs. Mechanisms that define TAD boundaries and the biological functions of TADs have been elusive. We analyzed chromosome architecture and its impact on gene expression during C. elegans X-chromosome dosage compensation. A condensin dosage compensation complex (DCC) binds to both hermaphrodite X chromosomes via rex sites (recruitment elements on X) to reduce transcription by half, while also establishing an X structure composed of TADs. Without DCC binding, eight TAD boundaries are lost, causing X structure to resemble that of autosomes. We defined the requirements for creating a DCC-dependent TAD boundary by making a series of rex deletions and insertions and measuring chromosome structure. Each rex deletion eliminated the associated DCC-dependent TAD boundary, revealing that a high-occupancy rex site is necessary for boundary formation. Inserting a rex site at a new location on X defined a new boundary, indicating that DCC binding at a high-occupancy rex site is sufficient to define the boundary. Deleting all eight rex sites at the eight DCC-dependent boundaries recapitulated the TAD structure of a DCC mutant. These 8rex? animals allowed us to measure transcription when TAD structure was grossly disrupted across an entire metazoan chromosome, but DCC binding was largely intact, and X chromosomes were properly compacted. The 8rex? worms lacked canonical dosage compensation phenotypes, and embryos did not show statistically significant changes in X-chromosome expression, indicating that TAD structure does not underlie the mechanism of dosage compensation. The absence of TADs allowed us to identify additional DCC-mediated X-chromosome structure that may underlie X compaction and facilitate transcriptional repression. Strikingly, though TADs do not mediate dosage compensation, abrogating TAD structure in hermaphrodites did reduce thermotolerance, accelerate aging, and shorten lifespan, implicating higher-order chromosome structure in regulating stress responses and aging. Our discoveries offer new directions for understanding the regulation of lifespan and the connection between chromosome organization and gene regulation.

Saiki R et al. (2008) Aging Cell "Altered bacterial metabolism, not coenzyme Q content, is responsible for the lifespan extension in Caenorhabditis elegans fed an Escherichia coli diet lacking coenzyme Q."

Saiki R, Clarke CF, Furukawa S, Larsen PL, Bixler T, Lunceford AL, Lee W, Dang P

[Aging Cell, 2008]

Coenzyme Qn is a fully substituted benzoquinone containing a polyisoprene tail of distinct numbers (n) of isoprene groups. C. elegans fed E. coli devoid of Q(8) have a significant life span extension when compared to C. elegans fed a standard "Q-replete"E. coli diet. Here we examine possible mechanisms for the life span extension caused by the Q-less E. coli diet. A bioassay for Q uptake shows that a water-soluble formulation of Q(10) is effectively taken up by both clk-1 mutant and wild-type nematodes, but does not reverse life span extension mediated by the Q-less E. coli diet, indicating that life span extension is not due to the absence of dietary Q per se. The enhanced longevity mediated by the Q-less E. coli diet cannot be attributed to dietary restriction, different Qn isoforms, reduced pathogenesis or slowed growth of the Q-less E. coli, and in fact requires E. coli viability. Q-less E. coli have defects in respiratory metabolism. C. elegans fed Q-replete E. coli mutants with similarly impaired respiratory metabolism due to defects in complex V also show a pronounced life span extension, although not as dramatic as those fed the respiratory deficient Q-less E. coli diet. The data suggest that feeding respiratory incompetent E. coli, whether Q-less or Q-replete, produces a robust life extension in wild-type C. elegans. We believe the fermentation-based metabolism of the E. coli diet is an important parameter of C. elegans longevity.

Eve A (2021) Development "An interview with Swathi Arur."

Eve A

[Development, 2021]

Swathi Arur is an Associate Professor for the Department of Genetics at the MD Anderson Cancer Center, USA, where she uses multidisciplinary approaches to understand female germline development and fertility. She has received numerous accolades, including the MD Anderson Distinguished Research Faculty Mentor Award in 2017. In 2020, she was elected to the American Association for the Advancement of Science (AAAS). Swathi joined the team at Development as an Academic Editor in 2020, and we met with her over Zoom to hear more about her life, her career and her love for <i>C. elegans</i>.

Govindan JA et al. (2015) Proc Natl Acad Sci U S A "Dialogue between E. coli free radical pathways and the mitochondria of C. elegans."

Mylonakis E, Govindan JA, Zhang X, Ruvkun G, Jayamani E

[Proc Natl Acad Sci U S A, 2015]

The microbial world presents a complex palette of opportunities and dangers to animals, which have developed surveillance and response strategies to hints of microbial intent. We show here that the mitochondrial homeostatic response pathway of the nematode Caenorhabditis elegans responds to Escherichia coli mutations that activate free radical detoxification pathways. Activation of C. elegans mitochondrial responses could be suppressed by additional mutations in E. coli, suggesting that C. elegans responds to products of E. coli to anticipate challenges to its mitochondrion. Out of 50 C. elegans gene inactivations known to mediate mitochondrial defense, we found that 7 genes were required for C. elegans response to a free radical producing E. coli mutant, including the bZip transcription factor atfs-1 (activating transcription factor associated with stress). An atfs-1 loss-of-function mutant was partially resistant to the effects of free radical-producing E. coli mutant, but a constitutively active atfs-1 mutant growing on wild-type E. coli inappropriately activated the pattern of mitochondrial responses normally induced by an E. coli free radical pathway mutant. Carbonylated proteins from free radical-producing E. coli mutant may directly activate the ATFS-1/bZIP transcription factor to induce mitochondrial stress response: feeding C. elegans with H2O2-treated E. coli induces the mitochondrial unfolded protein response, and inhibition of a gut peptide transporter partially suppressed C. elegans response to free radical damaged E. coli.

Yuen, Grace J. et al. (2013) International Worm Meeting "Enterococcus infection of C. elegans as a model of innate immunity."

Yuen, Grace J., Ausubel, Frederick M.

[International Worm Meeting, 2013]

Enterococcus is a Gram-positive commensal that is also an important opportunistic pathogen. Most human enterococcal infections are caused by either E. faecalis or E. faecium. Our laboratory has modeled Enterococcus infection in C. elegans using both species. We have previously shown that infection with either species leads to gut distention, but only E. faecalis is able to establish a persistent and lethal infection in the nematode. We now provide evidence that at least three canonical C. elegans immune signaling pathways are important for survival during infection with E. faecalis and E. faecium. While the lifespan of wild-type worms is unaffected by E. faecium infection, mutations in the PMK-1, FSHR-1, and BAR-1 immune signaling pathways lead to an immunocompromised phenotype. This new finding suggests that an active host response is required to keep E. faecium infection "in check" in the worm intestine. To further characterize the C. elegans host response to Enterococcus infections, we used genome-wide transcriptional profiling of nematodes feeding on E. faecalis and E. faecium, as well as two controls, heat-killed E. coli and live Bacillus subtilis, a non-pathogenic Gram-positive. We found that relative to B. subtilis, E. faecalis and E. faecium caused the upregulation of 249 and 166 genes, respectively, of which 105 genes were common to both, comprising the Enterococcus gene signature. Shared by both Enterococcus infection signatures were genes relating to oxidation/reduction, acyl-CoA dehydrogenase/oxidase activity, fatty acid metabolism, and C-type lectins. Additionally, the Enterococcus infection gene signature is fairly distinct from the P. aeruginosa, S. aureus, and C. albicans infection signatures. Furthermore, of the 91 genes that are upregulated in E. faecalis (more virulent) relative to E. faecium (less virulent), 22 are shared with the 77 genes upregulated in worms infected with virulent Microbacterium nematophilum relative to avirulent M. nematophilum (O'Rourke et al., 2006), suggesting that these genes may comprise a "virulence response signature." Studies are underway in understanding the biology of Enterococcus infection in C. elegans and identifying novel Enterococcus-activated pathways.

Harrington LA et al. (1988) Mech Ageing Dev "Effect of vitamin E on lifespan and reproduction in Caenorhabditis elegans."

Harrington LA, Harley CB

[Mech Ageing Dev, 1988]

Vitamin E extends the lifespan of many animals, including the nematode Caenorhabditis elegans. Our results confirm previous studies that 200 micrograms/ml vitamin E significantly prolonged C. elegans survival (17-23%, P less than 0.05) when added from hatching to day 3, while continuous exposure, either at hatching or from 4 days prior to hatching, had little additional effect. Treatment with 100 or 400 micrograms/ml vitamin E, or with other antioxidants (80 micrograms/ml vitamin C, either alone or in combination with vitamin E, or 120 micrograms/ml N,N'-diphenyl-1,4-diphenylenediamine (DPPD] did not significantly affect lifespan. All treatments with 200 micrograms/ml vitamin E moderately reduced fecundity (total progeny) and increased the mean day of reproduction. At 400 micrograms/ml, vitamin E had severe effects, while DPPD, vitamin C, and 100 micrograms/ml vitamin E had slight effects on both these parameters of reproduction. These data suggest that vitamin E increases lifespan in C. elegans in part by slowing development in the same manner that metabolic-depressant or mildly cytotoxic drugs increase lifespan, decrease fecundity, and delay the timing of reproduction.

Ryoichi Saiki et al. (2008) C.elegans Aging, Stress, Pathogenesis, and Heterochrony Meeting "Caenorhabditis elegans lifespan is profoundly modulated by its diet of E. coli: What are the roles of E. coli metabolism and coenzyme Q?"

Peter Dang, Tarra Bixler, Catherine Clarke, Pamela Larsen, Ryoichi Saiki, Adam Lunceford, Wendy Lee

[C.elegans Aging, Stress, Pathogenesis, and Heterochrony Meeting, 2008]

Coenzyme Qn is a fully substituted benzoquinone containing a polyisoprene tail of distinct numbers (n) of isoprene groups. Q is an essential component of respiratory electron transport and a potent lipid soluble antioxidant. Extended lifespans are observed in C. elegans clk-1 mutants with defects in Q biosynthesis. Intriguingly, mice heterozygous for a clk-1 gene disruption also show increased lifespan. C. elegans fed E. coli devoid of Q8 have a significant life span extension when compared to C. elegans fed a standard Q-replete E. coli diet. These results initially suggested that the lack of Q is the important parameter affecting lifespan. However, recent results indicate that feeding respiratory incompetent E. coli, whether Q-replete or Q-less, produces a robust lifespan extension in C. elegans. C. elegans skn-1 mutants fed the respiratory incompetent E. coli diets also show lifespan extension, suggesting that the response is independent of a dietary restriction effect. The respiratory incompetent E. coli diet may be imposed well after the worms reach adulthood, including post-reproductive adults, indicating that lifespan extension operates independently of worm development. Curiously, C. elegans fed the Q-less E. coli diet seem to exhibit more pronounced lifespan extension than when fed respiratory incompetent E. coli that are Q-replete. C. elegans ttx-3 mutants, harboring defects in the gene encoding a LIM homeodomain transcription factor, fail to distinguish the Q-less from the Q-replete respiratory defective E. coli. The difference in life span extension mediated by the two respiratory deficient E. coli diets depends on normal food seeking behavior exhibited by N2 C. elegans. The data suggest that the life span extension of N2 worms fed Q-less E. coli diet is caused by a combination of respiratory deficiency of the E. coli and the food seeking behavior of C. elegans. This work was supported by NIA Grant AG19777, and by the Ellison Medical Foundation.

BC Prasad et al. (1999) International C. elegans Meeting "The unc-3 locus encodes an O/E transcription factor, CeO/E, which is required for axonal guidance and chemosensory function."

BC Prasad, RR Reed

[International C. elegans Meeting, 1999]

The O/E family of rHLH transcription factors has been implicated in neurogenesis, axonal pathfinding, muscle formation and B cell maturation. The murine O/E proteins are expressed transiently in the developing CNS and PNS during times of axonogenesis and are expressed in olfactory neurons throughout development where they may regulate components of the olfactory signaling cascade. We have identified a C. elegans O/E homologue (CeO/E) that is encoded by the unc-3 locus. Unc-3 mutants display an uncoordinated phenotype attributed to a severe defasiculation and miswiring of the ventral cord (VNC). Using a GFP fusion to the unc-3 promoter and specific antibodies, we observed that CeO/E is expressed transiently in the excitatory VNC motor neurons and throughout development in a pair of chemosensory neurons (ASI amphid neurons). Several observations suggest that the protein may have distinct roles in the two cell types. Although the axonal and dendritic projections of the ASI appear to be normal when labeled with DiI, unc-3 mutants enter the dauer pathway under inappropriate conditions. Although CeO/E possesses highly conserved domains associated with DNA binding in the mammalian homologue, identification of DNA binding sites for the C. elegans protein has not been achieved. We have shown that CeO/E protein can homodimerize in vitro, although the DNA binding specificity of CeO/E is distinct from the mammalian O/E proteins. Several unc-3 target genes ( daf-7, unc-17/cha-1, unc-4 ) have been identified by other laboratories and each contains a mammalian binding site in the promoter region. Remarkably, we have been unable to demonstrate CeO/E binding at these sites. We are generating chimeras of O/E-1 and CeO/E to understand the DNA binding specificity of the CeO/E protein and utilizing a yeast-2-hybrid screen with both O/E-1 and CeO/E to identify interacting proteins in C. elegans . These studies should reveal the mechanism of CeO/E transcriptional activation and target gene regulation.

Garsin DA et al. (2001) Proc Natl Acad Sci U S A "A simple model host for identifying Gram-positive virulence factors."

Mylonakis E, Ausubel FM, Singh KV, Sifri CD, Calderwood SB, Murray BE, Qin X, Garsin DA

[Proc Natl Acad Sci U S A, 2001]

We demonstrate the use of the nematode Caenorhabditis elegans as a facile and inexpensive model host for several Gram-positive human bacterial pathogens. Enterococcus faecalis, Streptococcus pneumoniae, and Staphylococcus aureus, but not Bacillus subtilis, Enterococcus faecium, or Streptococcus pyogenes, kill adult C elegans. Focusing our studies on the enterococcal species, we found that both E. faecalis and E. faecium kill C elegans eggs and hatchlings, although only E. faecalis kills the adults. In the case of adults, a low inoculum of E, faecalis grows to a high titer in the C elegans intestine, resulting in a persistent infection that cannot be eradicated by prolonged feeding on E. faecium. Interestingly, a high titer of E. faecium also accumulates in the nematode gut, but does not affect the longevity of the worms. Two E. faecalis virulence-related factors that play an important role in mammalian models of infection, tsr, a putative quorum-sensing system, and cytolysin, are also important for nematode killing. We exploit the apparent parallels between Gram-positive infection in simple and more complex organisms by using the nematode to identify an E. faecalis virulence factor, ScrB, which is relevant to mammalian pathogenesis.

Zuckerman BM et al. (1983) Age "Effects of vitamin E on the nematode C. elegans."

Zuckerman BM, Geist MA

[Age, 1983]

Vitamin E at 200 ug/ml significantly extended the mean lifespan and extended maximum lifespan of the nematode Caenorhabditis elegans when supplied early in the prereproductive stage. At this concentration, vitamin E increased growth, but did not affect fecundity or the length of the reproductive period. The vitamin E effect was not passed from the parents to the progeny. Evaluations of the effects of vitamin E on lipofuscin accumulation were inconclusive. The results are compared to previous studies on C. briggsae and Turbatrix aceti.