Charles C Keller et al. (2005) International Worm Meeting "Identification and characterization of new mec-3 regulated genes in the touch receptor neurons."

Denis Dupuy, Marc Vidal, Martin Chalfie, Charles C Keller

[International Worm Meeting, 2005]

Six touch receptor neurons are responsible for sensing gentle touch to the body of C. elegans. Saturating mutageneses identified a handful of genes needed for the appropriate development and function of these touch neurons. Mutations in these genes lead to a mechanosensitive abnormal or Mec phenotype. Among the identified mec genes is the LIM-Homeobox transcription factor mec-3 which, in conjunction with its dimerization partner unc-86, regulates the expression of several other mec genes and appears to be the final determinant of touch neuron cell fate. Previous work, using isolated touch neurons and DNA microarrays identified 71 putative mec-3-dependent genes [Zhang et al. (2002) Nature 418: 331-335]. We have created promoter gfp fusion constructs for these transcripts and analyzed the resulting expression patterns in both wild-type and mec-3 backgrounds. We have confirmed seven new genes as being regulated by mec-3 (bringing the total to 21). Thirty-five genes are either false positives (they are not mec-3-dependent or noticeably expressed in wild-type touch neurons) or are regulated through cis elements outside the 5 noncoding sequence. Fifteen genes remain to be characterized (many of these are ribosomal subunit proteins that are difficult to characterize). The new mec-3-dependent genes are cct-1, encoding a T-complex chaperonin; cap-1, encoding a subunit of the f-actin capping complex; the acid phosphatase gene F14E5.4; the putative NADH dehydrogenase subunit gene F42A9.9; aip-1, a gene implicated in resistance to arsenic toxicity; and two genes of unknown function (F10A3.11 and T04B2.3). We are currently studying the roles of these and other mec-3-dependent genes in touch neuron development and function. For example, the generation of dsRNA for cct-4 (using a vector made by Chuck Ma that has the mec-18 and heat shock promoters in opposite orientations) causes touch insensitivity. The Zhang et al. microarray data also identified 25 genes that might be downregulated by mec-3 in the touch neurons. All these genes appear to be false negatives. We do not see expression in the mec-3 touch neurons."

Avery L et al. (2021) PLoS Comput Biol "A Keller-Segel model for C elegans L1 aggregation."

Dumur C, Artyukhin A, Ingalls B, Avery L

[PLoS Comput Biol, 2021]

We describe a mathematical model for the aggregation of starved first-stage C elegans larvae (L1s). We propose that starved L1s produce and respond chemotactically to two labile diffusible chemical signals, a short-range attractant and a longer range repellent. This model takes the mathematical form of three coupled partial differential equations, one that describes the movement of the worms and one for each of the chemical signals. Numerical solution of these equations produced a pattern of aggregates that resembled that of worm aggregates observed in experiments. We also describe the identification of a sensory receptor gene, srh-2, whose expression is induced under conditions that promote L1 aggregation. Worms whose srh-2 gene has been knocked out form irregularly shaped aggregates. Our model suggests this phenotype may be explained by the mutant worms slowing their movement more quickly than the wild type.

Zhang S et al. (2004) Curr Biol "MEC-2 is recruited to the putative mechanosensory complex in C. elegans touch receptor neurons through its stomatin-like domain."

Chalfie M, Caldwell GA, Yao CA, Arnadottir J, Keller C, Zhang S

[Curr Biol, 2004]

Background: The response to gentle body touch in C. elegans requires a degenerin channel complex containing four proteins (MEC-2, MEC-4, MEC-6, and MEC-10). The central portion of the integral membrane protein MEC-2 contains a stomatin-like region that is highly conserved from bacteria to mammals. The molecular function of this domain in MEC-2, however, is unknown. Results: Here, we show that MEC-2 colocalizes with the degenerin MEC-4 in regular puncta along touch receptor neuron processes. This punctate localization requires the other channel complex proteins. The stomatin-like region of MEC-2 interacts with the intracellular cytoplasmic portion of MEC-4. Missense mutations in this region that destroy the interaction also disrupt the punctate localization and degenerin-regulating function of MEC-2. Missense mutations outside this region apparently have no effect on the punctate localization but significantly reduce the regulatory effect of MEC-2 on the MEC-4 degenerin channel. A second stomatin-like protein, UNC-24, colocalizes with MEC-2 in vivo and coimmunoprecipitates with MEC-2 and MEC-4 in Xenopus oocytes; unc-24 enhances the touch insensitivity of temperature-sensitive alleles of mec-4 and mec-6. Conclusion: Two stomatin homologs, MEC-2 and UNC-24, interact with the MEC-4 degenerin through their stomatin-like regions, which act as protein binding domains. At least in the case of MEC-2, this binding allows its nonstomatin domains to regulate channel activity. Stomatin-like regions in other proteins may serve a similar protein binding function.

Keller, Martin et al. (2013) International Worm Meeting "Post-transcriptional control of C. elegans germ cell apoptosis by RNA-binding proteins."

Hengartner, Michael O., Keller, Martin

[International Worm Meeting, 2013]

Post-transcriptional control of mRNAs by RNA-binding proteins (RBPs) has a prominent role in the regulation of gene expression. RBPs interact with mRNAs to control their biogenesis, splicing, transport, localization, translation and stability. Defects in such regulation can lead to a wide range of human diseases from neurological disorders to cancer. Many fundamental biological pathways related to such disorders are conserved between Caenorhabditis elegans and humans. Therefore, studying RBPs associated with apoptosis in C. elegans could potentially give insight into processes underlying human diseases. Several RBPs are known to regulate apoptosis in the adult C. elegans germline. How these RBPs control apoptosis is however largely unknown. To gain a more comprehensive understanding of the general involvement of RBPs in the regulation of germ cell apoptosis, we performed an RNAi screen to identify novel RBP candidates that affect germ cell death. We verified our RNAi results via loss-of-function mutants and focus on the following confirmed candidates: glh-1, wago-4 and wago-5. In order to understand how these RBPs control apoptosis, the target mRNAs and the RNA-binding motifs will be identified with the recently developed in-vivo PAR-CLIP technique. Furthermore, RBP-protein interaction will be dissected using co-immunoprecipitation experiments. Our approach will allow us to build up a model of the germ cell apoptosis RNA regulon and broaden our understanding on how RBPs orchestrate cellular events.

Zhao Y et al. (2007) BMC Genomics "Poly-G/poly-C tracts in the genomes of Caenorhabditis."

Zhao Y, O'Neil NJ, Rose AM

[BMC Genomics, 2007]

ABSTRACT: BACKGROUND: In the genome of Caenorhabditis elegans, homopolymeric poly-G/poly-C tracts (G/C tracts) exist at high frequency and are maintained by the activity of the DOG-1 protein. The frequency and distribution of G/C tracts in the genomes of C. elegans and the related nematode, C. briggsae were analyzed to investigate possible biological roles for G/C tracts. RESULTS: In C. elegans, G/C tracts are distributed along every chromosome in a non-random pattern. Most G/C tracts are within introns or are close to genes. Analysis of SAGE data showed that G/C tracts correlate with the levels of regional gene expression in C. elegans. G/C tracts are over-represented and dispersed across all chromosomes in another Caenorhabditis species, C. briggase. However, the positions and distribution of G/C tracts in C. briggsae differ from those in C. elegans. Furthermore, the C. briggsae dog-1 ortholog CBG19723 can rescue the mutator phenotype of C. elegans dog-1 mutants. CONCLUSIONS: The abundance and genomic distribution of G/C tracts in C. elegans, the effect of G/C tracts on regional transcription levels, and the lack of positional conservation of G/C tracts in C. briggsae suggest a role for G/C tracts in chromatin structure but not in the transcriptional regulation of specific genes.

Bhagwati P Gupta et al. (2002) West Coast Worm Meeting "Genetic analysis of the vulval mutants in C. briggsae"

Shahla Gharib, Bhagwati P Gupta, Paul W Sternberg, Jennifer X Li

[West Coast Worm Meeting, 2002]

To understand the evolution of developmental mechanisms, we are doing a comparative analysis of vulval patterning in C. elegans and C. briggsae. C. briggsae is closely related to C. elegans and has identical looking vulval morphology. However, recent studies have indicated subtle differences in the underlying mechanisms of development. The recent completion of C. briggsae genome sequence by the C. elegans Sequencing Consortium is extremely valuable in identifying the conserved genes between C. elegans and C. briggsae.

Antika TR et al. (2023) J Biol Chem "Sequence-specific targeting of C. elegans C-Ala to the D-loop of tRNAAla."

Horng JC, Hsu HL, Nazilah KR, Wang CC, Wang TL, Wang SC, Antika TR, Chuang TH, Chrestella DJ, Wang SW, Tseng YK, Pan HC

[J Biol Chem, 2023]

Alanyl-tRNA synthetase (AlaRS) retains a conserved prototype structure throughout its biology. Nevertheless, its C-terminal domain (C-Ala) is highly diverged and has been shown to play a role in either tRNA or DNA binding. Interestingly, we discovered that Caenorhabditis elegans cytoplasmic C-Ala (Ce-C-Ala_c) robustly binds both ligands. How Ce-C-Ala_c targets its cognate tRNA and whether a similar feature is conserved in its mitochondrial counterpart remain elusive. We show that the N- and C-terminal subdomains of Ce-C-Ala_c are responsible for DNA and tRNA binding, respectively. Ce-C-Ala_c specifically recognized the conserved invariant base G¹⁸ in the D-loop of tRNA^Ala through a highly conserved lysine residue, K934. Despite bearing little resemblance to other C-Ala domains, C. elegans mitochondrial C-Ala (Ce-C-Ala_m) robustly bound both tRNA^Ala and DNA and maintained targeting specificity for the D-loop of its cognate tRNA. This study uncovers the underlying mechanism of how C. elegans C-Ala specifically targets the D-loop of tRNA^Ala.

Blumenthal TE et al. (1994) Worm Breeder's Gazette "C. elegans U2AF 65."

Zorio DAR, Lea K, Blumenthal TE

[Worm Breeder's Gazette, 1994]

C. elegans U2AF65

Oomura, S. et al. (2019) International Worm Meeting "Early embryogenesis of C. inopinata, a sibling species of C.elegans."

Matsumura, Y., Haruta, N., Hoshi, Y., Sugimoto, A., Oomura, S.

[International Worm Meeting, 2019]

C. inopinata is a newly discovered sibling species of C. elegans. Despite their phylogenetic closeness, they have many differences in morphology and ecology. For example, while C. elegans is hermaphroditic, C. inopinata is gonochoristic; C. inopinata is nearly twice as long as C. elegans. A comparative analysis of C. elegans and C. inopinata enables us to study how genomic changes cause these phenotypic differences. In this study, we focused on early embryogenesis of C. inopinata. First, by the microparticle bombardment method we made a C. inopinata line that express GFP::histone in whole body, and compared the early embryogenesis with C. elegans by DIC and fluorescent live imaging. We found that the position of pronuclei and polar bodies were different between these two species. In C. elegans, the female and male pronuclei first become visible in anterior and posterior sides, respectively, then they meet at the center of embryo. On the other hand, the initial position of pronuclei were more closely located in C. inopinata. Also, the polar bodies usually appear in the anterior side of embryo in C. elegans, but they appeared at random positions in C. inopinata. Therefore, we infer that C. inopinata may have a different polarity formation mechanism from that in C. elegans. We are also analyzing temperature dependency of embryogenesis in C. inopinata, whose optimal temperature is ~7 degree higher than that in C. elegans.

Guven K (1995) Journal of Thermal Biology "Differential expression of hsp70 proteins in response to heat and cadmium in Caenorhabditis elegans."

Guven K

[Journal of Thermal Biology, 1995]

1. The patterns of HSP70 expression induced in Caenorhabditis elegans by mild (31 degrees C) or severe (34 degrees C) heat shock, and by cadmium ions at 31 degrees C, have been compared with those expressed constitutively ill 20 degrees C controls by 1- and a-dimensional immunoblotting. 2. The 2D spot patterns become more complex with increasing severity of stress (34 degrees C > 31 degrees C + Cd > 31 degrees C > 20 degrees C). 3. A stress-inducible transgene construct is minimally active at 31 degrees C, but is abundantly expressed in the presence of cadmium or at 34 degrees C. 4. Differing degrees or types of stress may differentially induce available hsp70