Roussell DL et al. (1991) Worm Breeder's Gazette "Other Helicases We Have Cloned (Including an eIF-4A-like PCR Product From C. elegans)"

Bennett KL, Roussell DL, Christoffersen C

[Worm Breeder's Gazette, 1991]

With one set of primers designed to amplify the Drosophila vasa- equivalent from C. elegans, we produced several distinct PCR products. Because these primer sequences were not unique to the vasa sequence but rather were shared by all members of the so-called DEAD family of helicases, our results were not unexpected. We predicted that the different PCR products would correspond to different helicase protein genes. The multiple PCR amplified DNA fragments were gel isolated, cloned and sequenced. To date, sequence analyses of our PCR clones suggest that C. elegans may have as many as six different potential helicase protein genes that belong to the DEAD family of helicases ( Nature 335:611-617). Most of these represent potential helicases that have not been previously characterized in another organism. It may be possible to characterize a whole family of putative helicase genes in Caenorhabditis.One of our PCR clones, called NA9-1, has 61% perfect amino acid homology to eIF-4A, the protein synthesis initiation factor that has been cloned from mouse (Nielsen et al., NAR 13:6867-6880). The identity is 83% with conserved amino acid changes. Shown below is a comparison of NA9-1 predicted amino acid sequence with that of the mouse genes eIF-4AI/II and the yeast equivalents Tif1/2 (Linder and Slonimski, NAR 16:10359). There is 54% perfect amino acid homology between the C. elegans clone, NA9-1, and the yeast Tif1/2. The position of an intron whose exact location is conserved between the mouse and nematode sequences is also indicated. The eIF-4A protein is well characterized (for review see Moldave,K., Ann. Rev. Biochem. 54:1109-1149). It recognizes the 5' cap structure of RNAs, has RNA binding activity, and has an ATPase- dependent helicase activity upon RNAs. Some of the different helicase motifs that are conserved among this large class of proteins have been functionally analyzed with eIF-4A. The two genes eIF-4AI and II, although highly conserved, have different patterns and levels of expression in different tissues (Nielsen and Trachsel, EMBO J. 7:2097- 2105). We are not yet certain if there are multiple Caenorhabditis eIF-4A-like genes. There are two EcoRI fragments of C. elegans DNA, 2.4 Kb and 1.3 Kb, that hybridize to the insert of NA9-1 on genomic Southerns, but there is also an EcoRI site in our PCR clone. In addition, the small size and unequal hybridization signals of the two genomic EcoRI fragments does not distinguish between a single gene or multiple highly conserved genes that corresponds to our PCR clone, NA9- 1. We have also used the NA9-1 insert DNA to isolate a cDNA from a C. elegans cDNA library previously constructed in this laboratory. We are currently completing the sequence analysis of this clone. Preliminary data show that the cDNA clone, called CEB1, corresponds to the amplified PCR product and that its homology at the amino acid level with eIF-4A extends outside the region delimited by the PCR primers. [See Figure 1]

Roussell DL et al. (1991) International C. elegans Meeting "CHARACTERIZATION OF SEVERAL PUTATIVE RNA HELICASE GENES, INCLUDING AN eIF-4A-LIKE GENE OF CAENORHABDITIS."

Roussell DL, Christoffersen C, Bennett KL, Gharib S

[International C. elegans Meeting, 1991]

With one set of primers designed to amplify the Drosophila vasaequivalent from C. elegans, we produced several distinct PCR products. Because these primer sequences were not unique to the vasa sequence but rather were shared by all members of the so-called DEAD family of helicases (Nature 335:611-617), our results were not unexpected. We predicted that the different PCR products would correspond to different helicase protein genes. The multiple PCR amplified DNA fragments were gel isolated, cloned and sequenced. To date, sequence analyses of our PCR clones suggest that C. elegans has at least six different potential helicase protein genes that belong to the DEAD family of helicases. Most of these represent potential helicases that have not been previously characterized in another organism. It may be possible to characterize a whole family of putative RNA helicase genes in Caenorhabditis. One of our PCR clones, called NA9- I, has conserved intron position and 61% perfect (83% conserved) amino acid homology to eIF-4A I&II, the protein synthesis initiation factor genes that have been cloned from mouse (Nielsen et al., NAR 13:6867-6880). The two mouse genes, eIF-4A I&II, although highly conserved, have different patterns and levels of expression in different tissues. (Nielsen and Trachsel, EMBO J. 7:20972105). We are not yet certain if there are multiple Caenorhabditis eIF4Alike genes. On genomic Southerns there are two EcoRI fragments of C. elegans DNA, 2.4Kb and 1.0Kb, that hybridize to the insert DNA of NA91. However, because there is an EcoRI site within the PCR clone, these results do not distinguish between a single gene or multiple highly conserved genes. By Northern analysis, a single 1. 8Kb RNA is detected. The mouse eIF-4A protein recognizes the 5'cap structure of RNAs, has RNA binding activity, and has an ATPase-dependent helicase activity upon RNAs. We plan to functionally assay the C. elegans putative eIF- 4A gene product by complementation in Saccharomyces cerevisiae. Linder et al. (PNAS 86:2286-2290) have constructed mutant strains of 5. cerevisiae to demonstrate that the yeast equivalents of eIF-4A, Tif 1&2, are essential and functionally identical genes. The C. elegans PCR clone, NA9-I, shares 54% amino acid sequence identity with Tif 1&2 (Linder and Slonimski, NAR 16:10359). Using the S. cerevisiae strains constructed and provided by Patrick Linder, we are attempting to complement the Tifl-/Tif2- mutant with a potentially full-length cDNA that we have isolated from a cDNA library provided by Stuart Kim and that corresponds to NA9- 1.

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

Xu J et al. (2018) J Nanosci Nanotechnol "Carbon Quantum Dots as Fluorescent Probes for Imaging and Detecting Free Radicals in C. elegans."

Wang Q, Guan S, Wang L, Wang M, Zhang Y, Mu Y, Xu J, Wang K, Li J

[J Nanosci Nanotechnol, 2018]

Uniform and hydrophilic carbon quantum dots (C-QDs) were synthesized by calcination and NaOH treatment from an organo-templated zeolite precursor. The color of luminescence was determined by the concentration of C-QDs. These variable-color C-QDs were applied for the first time in the imaging of Caenorhabditis elegans (C. elegans) as a model organism. The effects of C-QDs and possible behavioral changes in C. elegans were evaluated under treatment conditions. We could clearly observe distribution of C-QDs in C. elegans from the fluorescence images. Furthermore, we observed significant and detectable fluorescence quenching of the C-QDs by free radicals in C. elegans. Our work affirms that C-QDs can be developed as imaging probes and as potential fluorescent quantitative probes for detecting free radicals.

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

David Fitch, Karin Kiontke, Marie-Anne FELIX

[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.