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

Paul W Sternberg, Bhagwati P Gupta, Shahla Gharib, 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.

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

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

[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.

Davide Faggionato et al. (2006) European Worm Meeting "Learning Lessons from dys-1 and snf-6 - Having Acetylcholine as a Teacher"

Ralf Baumeister, Davide Faggionato, Oyunbileg Nyamsuren

[European Worm Meeting, 2006]

We study the function/dysfunction of mutations of genes that in humans have been associated with degenerative disorders. Recently, we identified components of an ubiquitylation complex as regulators of muscle assembly and turnover. Specifically, mutational inactivation of ubiquitylation suppressed paralysis of unc-45 mutant animals that show a severe myofibril disorganization 1.. In order to get an idea whether this is a generally applicable way to reduce the phenotypic consequences of mutations in muscle genes, we focused on other genes affecting muscle assembly and function.. dys-1 encodes the C. elegans orthologue of human dystrophin, mutations of the latter being responsible for Duchenne muscular dystrophy. One of the available mutants in dys-1, cx18, displays a surprisingly mild impairment of movement, that, however, is strongly enhanced in the background of hlh-1/MyoD, generating a synthetic paralysis. However, dys-1(cx18) animals also display subtle phenotypes like increased sensitivity to aldicarb, suggesting an additional neuronal function of this gene 2.. In a previous screen for ethanol resistance, mutations in the muscular sodium-acetylcholine cotransporter gene snf-6 were identified. Surprisingly, snf-6 mutations strongly resemble the dys-1 mutant phenotype in an hlh-1 background, suggesting a link between cholinergic signalling and dystrophin function.. In order to understand dys-1 dysfunction, we performed a detailed comparative analysis of both mutants and will present the data in our poster.. 1Hoppe T, Cassata G, Barral JM, Springer W, Hutagalung AH, Epstein HF, Baumeister R. Regulation of the myosin-directed chaperone UNC-45 by a novel E3/E4-multiubiquitylation complex in C. elegans. Cell. (2004) 118(3), 337-49. 2Bessou C, Giugia JB, Franks CJ, Holden-Dye L, Segalat L. Mutations in the Caenorhabditis elegans dystrophin-like gene dys-1 lead to hyperactivity and suggest a link with cholinergic transmission. Neurogenetics. 1998 Dec;2(1):61-72

Karin Kiontke et al. (2008) Development & Evolution Meeting "New Phylogeny Of Caenorhabditis Including Recently Discovered Species"

Marie-Anne FELIX, Karin Kiontke, David Fitch

[Development & Evolution Meeting, 2008]

Recently, seven new Caenorhabditis have been discovered, bringing the number of Caenorhabditis species in culture to 17, 10 of which are undescribed. To elucidate the relationships of the new species to the five species with sequenced genomes, we have used sequence data from two rRNA genes and several protein-coding genes for reconstructing the phylogenetic tree of Caenorhabditis. Four new species (spp. 5, 9, 10, 11) group within the so-called Elegans group of Caenorhabditis, with C. elegans being the first branch. Whereas none of them is likely to be the sister species of C. elegans, we now know of two close relatives of C. briggsae-C. sp. 5 and C. sp. 9. C. sp. 9 can hybridize with C. briggsae in the laboratory [see abstract by Woodruff et al.]. Of the remaining new species, C. sp. 7 branches off between C. elegans and C. japonica. This species is easier to cultivate than C. japonica and may be a better candidate for comparative experimental work. Two of the new species branch off before C. japonica as sister species of C. sp. 3 and C. drosophilae+C. sp. 2, respectively. Only one of the new species, C. sp. 11, is hermaphroditic. The position of C. sp. 11 in the phylogeny suggests that hermaphroditism evolved three times within the Elegans group. Two of the new species were isolated from rotting leaves and flowers, and five from rotting fruit. Rotting fruit is also the habitat in which C. elegans has been found to proliferate (Barriere and Felix, Genetics 2007) and from which C. briggsae, C. brenneri and C. remanei were repeatedly isolated. This suggests that the habitat of the stem species of Caenorhabditis after the divergence of the earliest branches (C. plicata, C. sonorae and C. sp. 1) was rotting fruit. The rate of discovery of new Caenorhabditis species has steadily increased since the description of C. elegans in 1899, with a leap in the last two years. There is no indication that we are even close to knowing all species in this genus.

Schartner, Caitlin M. et al. (2015) International Worm Meeting "X-chromosome evolution: divergence of X-sequence motifs that drive dosage compensation across Caenorhabditis species."

Lo, Te-Wen, Schartner, Caitlin M., Meyer, Barbara J.

[International Worm Meeting, 2015]

Dosage compensation (DC) across Caenorhabditis species exemplifies an essential process that has undergone rapid co-evolution of protein-DNA interactions central to its mechanism. In C. elegans, recruitment elements on X (rex sites) recruit a condensin-like DC complex (DCC) to hermaphrodite X chromosomes to balance gene expression between the sexes. Recruitment assays in vivo showed that C. elegans rex sites do not recruit the DCC of C. briggsae, and vice versa. To understand how DC complexes and X chromosomes evolved to use different X targeting sequences, we compared DCC subunits and binding sites in C. elegans to those in three species of the C. briggsae clade (15-30 MYR diverged): C. briggsae, its close relative C. nigoni (C. sp. 9), and C. tropicalis (C. sp. 11). By raising antibodies and introducing endogenous tags with TALENs or CRISPR/Cas9, we showed that homologs of both SDC-2, the pivotal X targeting factor, and DPY-27, a DCC-specific condensin subunit, bind X chromosomes of XX animals. Although the DCC shares key components across these four species, the binding sites differ. First, ChIP-seq studies in C. briggsae and C. nigoni identified DCC binding sites that are homologous across these close relatives but differ from C. elegans sites in sequence and location. Second, C. elegans sites use motifs enriched on X (MEX and MEXII) to drive DCC binding, but these motifs are not in C. briggsae or C. nigoni DCC sites and are not X-enriched. Third, we found an X-enriched motif at DCC binding sites of C. briggsae and C. nigoni that is not X-enriched in C. elegans. An oligo with the C. briggsae motif recruits the DCC in C. briggsae, but a similar oligo lacking the motif fails to recruit, establishing the importance of the motif. Fourth, another motif was found in C. briggsae and C. nigoni that shares a few nucleotides with MEX, but its functional divergence was shown by C. elegans recruitment assays. Fifth, two endogenous C. briggsae X-chromosome regions with strong C. elegans MEX motifs fail to recruit the C. briggsae DCC, as assayed by ChIP-seq and recruitment assays. None of these DCC motifs is enriched on the C. tropicalis draft X sequence, supporting further binding site divergence within the C. briggsae clade. Ongoing ChIP-seq studies in C. tropicalis will help determine how C. elegans and C. briggsae clade motifs are evolutionarily related. Comparison of DCC targeting mechanisms across these four species allows us to characterize a rarely captured event: the recent co-evolution of a protein complex and its rapidly diverged target sequences across an entire X chromosome.

Kiontke, Karin C. et al. (2009) International Worm Meeting "New Caenorhabditis species: phylogeny and evolution."

Fitch, David H. A., Felix, Marie-Anne, Kiontke, Karin C.

[International Worm Meeting, 2009]

Recently, nine new Caenorhabditis have been discovered, bringing the number of Caenorhabditis species in culture to nineteen, eleven of which are undescribed. To elucidate the relationships of the new species to the five species with sequenced genomes, we have used sequence data from two rRNA genes and several protein-coding genes for reconstructing the phylogenetic tree of Caenorhabditis. Four new species (spp. 5, 9, 10 and 11) group within the so-called Elegans group of Caenorhabditis, with C. elegans being the first branch. Although none of them is the sister species of C. elegans, C. sp. 5 and C. sp. 9 are close relatives of C. briggsae. C. sp. 9 can hybridize with C. briggsae in the laboratory. Of the remaining new species, C. sp. 7 branches off between C. elegans and C. japonica. Three of these species, C. sp. 7, C. sp. 9 and C. sp. 11 have been chosen for genome sequencing. Four further new species branch off before C. japonica within a monophyletic clade which also comprises C. sp. 3 and C. drosophilae. Only one of the new species, C. sp. 11, is hermaphroditic. The position of C. sp. 11 in the phylogeny suggests that hermaphroditism evolved three times within the Elegans group. Two of the new species were isolated from rotting leaves and flowers, and seven from rotting fruit. Rotting fruit is also the habitat in which C. elegans has been found to proliferate (Barriere and Felix, Genetics 2007) and from which C. briggsae, C. brenneri and C. remanei were repeatedly isolated. This suggests that the habitat of the stem species of Caenorhabditis after the divergence of the earliest branches (C. plicata, C. sonorae and C. sp. 1) was rotting fruit. Other characters, like the shape of the stoma and the male tail, introns, susceptibility to RNAi and genome size are being evaluated in the context of the phylogeny. The rate of discovery of new Caenorhabditis species has steadily increased since the description of C. elegans in 1899, with a leap in the last few years. There is no indication that we are even close to knowing all species in this genus.

Xiaodong Wang et al. (2003) International Worm Meeting "Evolution of a novel gene expression pattern in C. elegans"

Xiaodong Wang, Helen M Chamberlin

[International Worm Meeting, 2003]

Previous studies have shown that C. elegans ovo-related gene lin-48 expresses in a small number of cells including the excretory duct cell. In the related species C. briggsae, the expression is conserved in all cells except the excretory duct. This lin-48 expression difference affects excretory duct morphogenesis. In C. briggsae, as well as in C. elegans lin-48(sa496) mutants, the excretory duct is more anterior than in C. elegans wild type. This indicates that C. elegans lin-48 (Ce-lin-48) is involved in duct morphogenesis and positioning, but this gene function is absent in C. briggsae (1). We have made reporter transgenes composed of the lin-48 regulatory sequences from C. elegans or C. briggsae driving expression of green fluorescent protein (GFP). Tests of these clones in each species showed that only the Ce-lin-48 is expressed in excretory duct cell in C. elegans animal. These results indicate that there are differences in both cis-regulatory sequences and trans-acting proteins between the two species. By creating chimeric reporter transgenes including C. elegans and C. briggsae regulatory sequences, we have found that one difference between the two species is the presence of regulatory sequences in Ce-lin-48 that respond to the bZip protein CES-2 (1). The lin-48 gene expression differences between C. elegans and C. briggsae could result from loss of excretory duct expression in the C.briggsae lineage or acquired expression in the C. elegans lineage. To distinguish between these possibilities, we have analyzed three additional Caenorhabditis species (C. remanei, C. sp. CB5161 and C. sp. PS1010). We found these species have a duct morphology similar to C. briggsae indicating the C. elegans morphology is unique to this species. For comparison to C. elegans and C. briggsae, we have isolated the lin-48 gene from C. remanei and C. sp. CB5161. Alignment of the lin-48 regulatory sequences reveals that the sequences are more conserved among C. briggsae, C. remanei and C. sp. 5161. Several conserved domains are absent from C. elegans, whereas the previously identified CES-2 binding sites are absent from the other species. Currently, we are creating lin-48::gfp reporter transgenes for each species to observe the gene expression patterns. Further experiments with these transgenes will allow us to test whether the differences between C. elegans and the other species result from a loss of repressor elements or gain of activator elements in the C. elegans gene. (1)X. Wang and H. M. Chamberlin (2002) Genes & Development 16: 2345-2349.

AJ Wright et al. (1999) International C. elegans Meeting "Functions of C. elegans cell fate determining genes in C. briggsae"

CP Hunter, AJ Wright

[International C. elegans Meeting, 1999]

We are investigating the conservation of function of SKN-1 and PAL-1 between C. elegans and C. briggsae . In C. elegans , skn-1 is required to specify the EMS fate and pal-1 is required to specify the C and D fates. We have identified C. briggsae skn-1 and pal-1 homologues and are using RNA mediated interference (RNAi) to inhibit their function in C. briggsae . To assist in our phenotypic characterization we are identifying tissue specific antibodies that cross react with C. briggsae and ablating early blastomeres to ensure that C. briggsae early development does not differ substantially from that of C. elegans . Our preliminary results are encouraging. We have identified several monoclonal antibodies that cross react with C. briggsae antigens. These include 3NB12 which recognizes pharynx muscle, 5-6 which recognizes body wall muscle, J126 which recognizes intestinal cells and intestinal valve cells, and MH-27 which recognizes adherence junctions. Ablation experiments on early C. briggsae embryos have not yet indicated any obvious differences in cell fate between C. briggsae and C. elegans . Likewise blastomere interactions important in the early C. elegans embryo, like that of MS signaling to ABa at the 12 cell stage to promote pharynx formation in ABa, also appear to be required. C. briggsae pal-1 (RNAi) produces dead embryos with an overall gross morphology different from that of C. elegans pal-1 (RNAi) embryos. Preliminary characterization indicates that while C. elegans pal-1 function is restricted to specifying C and D blastomere fates, C. briggsae pal-1 function may be more broadly required. Future work will focus on investigating the C. briggsae pal-1 (RNAi) phenotype more thoroughly and cloning and performing similar experiments on the SKN-1 homologue.

Sugimoto, Asako et al. (2017) International Worm Meeting "Establishing genetic techniques to study Caenorhabditis sp. 34, a sister species of C. elegans."

Hoshi, Yuki, Namai, Satoshi, Kumagai, Ryohei, Kanzaki, Natsumi, Kikuchi, Taisei, Tsuyama, Kenji, Sugimoto, Asako

[International Worm Meeting, 2017]

Caenorhabditis sp. 34 is a sister species of C. elegans recently isolated from the syconia of the fig Ficus septica on Ishigaki Island, Japan (see abstract by T. Kikuchi, et al.). C. sp. 34 is gonochoric and shares typological key characters with other Elegans supergroup species, but strikingly, adults are nearly twice as long as C. elegans. The optimal culture temperature for C. sp. 34 is significantly higher (27 deg C) than that of C. elegans (20 deg C). Young adult males and females tend to form clumps, and Dauer larvae are rarely observed in laboratory culture conditions. Recently the C. sp. 34 genome assembly was produced into six chromosomes (see abstract by T. Kikuchi, et al.). The marked differences from C. elegans in morphology, behaviors and ecology, and the availability of the complete genome sequence make C. sp. 34 highly attractive for comparative and evolutionary studies. To make C. sp. 34 genetically tractable, we have been developing genetic and molecular techniques and tools. Stable transgenic lines of C. sp.34 could be obtained by microinjecting marker plasmids commonly used in C. elegans, although the efficiency was lower than that in C. elegans. Both soaking and feeding RNAi was as effective as in C. elegans. A panel of antibodies against C. elegans proteins successfully recognized expected structures in C. sp. 34 by immunofluorescence. Thus, many of the rich genetic and molecular resources for C. elegans can be directly used for C. sp. 34 studies. We well present some of the comparative analyses of gene functions regarding the body size, germ cell formation and sex determination.

Oyunbileg Nyamsuren et al. (2006) European Worm Meeting "Down-Regulation of CHN-1, a Chaperone-Associated E3-Ligase, Suppresses Muscle Degeneration in DMD Model of C. elegans"

Ralf Baumeister, Oyunbileg Nyamsuren

[European Worm Meeting, 2006]

CHN-1, the C. elegans ortholog of human CHIP (carboxyl terminus of HSC70-interacting protein), is a chaperone-associated ubiquitin ligase, which mediates the attachment of a ubiquitin chain to a client protein and thereby stimulates its degradation by proteasome. Recently, C. elegans CHN-1 in a complex with ubiquitin conjugating enzyme UFD-2, was reported to multiubiquitylate myosin chaperone UNC-45 and the absence of CHN-1 partially suppress myofibril disorganization and paralysis phenotype of unc-45 mutants (ref.). Since ubiquitin-proteasome system is the major protein degradation pathway in muscle cells (1), we started to analyse other C. elegans mutants that have been associated with defective muscle structures or functions. Among these are mutations in dys-1, encoding the C. elegans homologue of human dystrophin. Mutations in dystrophin cause Duchenne muscular dystrophy. Previous experiments by the Segalat lab have shown that combining dystrophin and MyoD mutants in dys-1(cx18);hlh-1(cc561ts) animals results in a synthetic phenotype, causing muscle degeneration and immobility at late larval stages. Strikingly, our experiments indicate that inactivation of chn-1 -/- also is able to suppress the dystrophin phenotype, significantly reducing muscle decay and resulting in improved locomotion and egg-laying. A detailed analysis of the dystrophic phenotype of dys-1(cx18);hlh-1(cc561ts) animals revealed a loss of 13% of all body-wall muscles already at day 2 of adulthood, whereas muscle degeneration is reduced to 4% in animals with additional CHN-1 deficiency. As a consequence, the triple mutant animals perform remarkably better in a food race assay, an indicator of improved muscle activity. Our data suggest that the precise regulation of proteolysis in the muscle may be an effective way to delay muscle degeneration in disease. Transcriptome profiling allowed us to identified genes that are either up- or downregulated as a consequence of the suppressor mutation. We are currently engaged in identifying their roles in this process. . 1Hoppe T, Cassata G, Barral JM, Springer W, Hutagalung AH, Epstein HF, Baumeister R. Regulation of the myosin-directed chaperone UNC-45 by a novel E3/E4-multiubiquitylation complex in C. elegans.Cell. (2004) 118(3), 337-49.