Li K et al. (2018) Environ Pollut "Assessing the influence of the genetically modified factor on mixture toxicological interactions in Caenorhabditis elegans: Comparison between wild type and a SOD type."

Liu SS, Li K, Feng L, Xu YQ

[Environ Pollut, 2018]

How to evaluate the ecological risk of transgenic technology is a focus of scientists because of the safety concerns raised by genetically modified (GM) organisms. Nevertheless, most studies are based on individual chemicals and always analyze the GM organism as a type of toxicant. In this study, we changed the approach and used GM organisms as the test objects with normal chemical exposure. Three types of chemicals (two substituted phenols, 4-chlorophenol and 4-nitrophenol; two ionic liquids, 1-butylpyridinium chloride and 1-butylpyridinium bromide; two pesticides, dichlorvos and glyphosate) were used to construct a six-component mixture system. The lethality to wild-type (N2) and sod-3::GFP (SOD-3) Caenorhabditis elegans was determined when they were exposed to the same mixture system after 12 and 24h. The results showed that the pEC50 values of all of the single chemicals on SOD-3 were greater than those on N2 at 24h. The toxicities of the single chemicals and nine mixture rays on the two strains increased with time. Notably, we discovered a significant difference between the two strains; time-dependent synergism occurred in mixtures on N2, but time-dependent antagonism occurred in mixtures on SOD-3. Finally, the strength of the synergism or antagonism turned to additive action on the two strains as the exposure time increased. These findings illustrated that the GM factor of the nematode influenced the mixture toxicological interaction at some exposure times. Compared with N2, SOD-3 were more sensitive to stress or toxic reactions. Therefore, the influence of the GM factor on mixture toxicological interactions in environmental risk assessment must be considered.

McIntyre LM et al. (2022) Sci Rep "GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease."

Huertas F, Miller GW, McIntyre LM, Murphy CT, Morse AM, Conesa A, Kaletsky R, Kalia V, Moskalenko O, Mor DE

[Sci Rep, 2022]

Parkinson's disease (PD) is a disabling neurodegenerative disorder in which multiple cell types, including dopaminergic and cholinergic neurons, are affected. The mechanisms of neurodegeneration in PD are not fully understood, limiting the development of therapies directed at disease-relevant molecular targets. C. elegans is a genetically tractable model system that can be used to disentangle disease mechanisms in complex diseases such as PD. Such mechanisms can be studied combining high-throughput molecular profiling technologies such as transcriptomics and metabolomics. However, the integrative analysis of multi-omics data in order to unravel disease mechanisms is a challenging task without advanced bioinformatics training. Galaxy, a widely-used resource for enabling bioinformatics analysis by the broad scientific community, has poor representation of multi-omics integration pipelines. We present the integrative analysis of gene expression and metabolite levels of a C. elegans PD model using GAIT-GM, a new Galaxy tool for multi-omics data analysis. Using GAIT-GM, we discovered an association between branched-chain amino acid metabolism and cholinergic neurons in the C. elegans PD model. An independent follow-up experiment uncovered cholinergic neurodegeneration in the C. elegans model that is consistent with cholinergic cell loss observed in PD. GAIT-GM is an easy to use Galaxy-based tool for generating novel testable hypotheses of disease mechanisms involving gene-metabolite relationships.

Abdelghany HM et al. (2003) J Biol Chem "Analysis of the catalytic and binding residues of the diadenosine tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans by site-directed mutagenesis."

McLennan AG, Rafferty JB, Bailey S, Blackburn GM, Abdelghany HM

[J Biol Chem, 2003]

The contributions to substrate binding and catalysis of 13 amino acid residues of the Caenorhabditis elegans diadenosine tetraphosphate pyrophosphohydrolase (Ap(4)A hydrolase) predicted from the crystal structure of an enzyme-inhibitor complex have been investigated by site-directed mutagenesis. Sixteen glutathione S-transferase-Ap(4)A hydrolase fusion proteins were expressed and their k(cat) and K-m values determined after removal of the glutathione S-transferase domain. As expected for a Nudix hydrolase, the wild type k(cat) of 23 s(-1) was reduced by 10(5)-, 10(3)-, and 30-fold, respectively, by replacement of the conserved P-phosphate-binding catalytic residues Glu(56), Glu(52), and Glu(103) by Gln. K-m values were not affected, indicating a lack of importance for substrate binding. In contrast, mutating His(31) to Val or Ala and Lys(83) to Met produced 10- and 16-fold increases in K. compared with the wild type value of 8.8 muM. These residues stabilize the P-1-phosphate. H31V and H31A had a normal kcat but K83M showed a 37-fold reduction in k(cat). Lys(36) also stabilizes the P-1-phosphate and a K36M mutant had a 10-fold reduced kcat but a relatively normal K-m. Thus both Lys(36) and Lys(83) may play a role in catalysis. The previously suggested roles of Tyr(27), His(38), Lys(79), and Lys(81) in stabilizing the P-2 and P-3-phosphates were not confirmed by mutagenesis, indicating the absence of phosphate-specific binding contacts in this region. Also, mutating both Tyr(76) and Tyr(121), which clamp one substrate adenosine moiety between them in the crystal structure, to Ala only increased K-m 4-fold. It is concluded that interactions with the P-1- and P-4-phosphates are minimum and sufficient requirements for substrate binding by this class of enzyme, indicating that

Bailey S et al. (2002) Acta Crystallogr D Biol Crystallogr "Crystallization of a complex of Caenorhabditis elegans diadenosine tetraphosphate hydrolase and a non-hydrolysable substrate analogue, AppCH2ppA."

Rafferty JB, McLennan AG, Abdelghany HM, Blackburn GM, Sedelnikova SE, Bailey S

[Acta Crystallogr D Biol Crystallogr, 2002]

The molecule diadenosine tetraphosphate (Ap(4)A) has been suggested to be a component of the cellular response to metabolic stress and/or, via the intracellular Ap(3)A/Ap(4)A ratio, to be involved in differentiation and apoptosis. Thus, the enzyme Ap(4)A hydrolase has a key metabolic role through regulation of the intracellular Ap(4)A levels. Crystals of this enzyme from the nematode Caenorhabditis elegans have been obtained in the presence of a non-hydrolysable substrate analogue, AppCH(2)ppA. The crystals belong to space group P2(1), unit-cell parameters a = 57.6, b = 36.8, c = 68.9 Angstrom, beta = 114.2degrees, and diffract to approximately 2.0 Angstrom. Determination of the structure of this complex will provide insights into the substrate specificity and catalytic activity of this class of enzymes.

Chuang P-T et al. (1996) Science "Sex-specific assembly of a dosage compensation complex on the nematode X chromosome."

Lieb JD, Meyer JB, Chuang P-T

[Science, 1996]

In nematodes, flies, and mammals, dosage compensation equalizes X-chromosome gene expression between the sexes through chromosome-wide regulatory mechanisms that function in one sex to adjust the levels of X-linked transcripts. Here, a dosage compensation complex was identified in the nematode Caenorhabditis elegans that reduces transcript levels from the two X chromosomes in hermaphrodites. This complex contains at least four proteins, including products of the dosage compensation genes dpy-26 and dpy-27. Specific localization of the complex to the hermaphrodite X chromosomes is conferred by XX-specific regulatory genes that coordinately control both sex determination and dosage compensation.AD - Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.FAU - Chuang, P TAU - Chuang PTFAU - Lieb, J DAU - Lieb JDFAU - Meyer, B JAU - Meyer BJLA - engID - GM30702/GM/NIGMSID - T32 GM07127/GM/NIGMSPT - Journal ArticleCY - UNITED STATESTA - ScienceJID - 0404511RN - 0 (Carrier Proteins)RN - 0 (DPY-27 protein)RN - 0 (Helminth Proteins)RN - 0 (Nuclear Proteins)RN - 0 (RNA, Helminth)RN - 0 (RNA, Messenger)SB - IM

Turaga PS et al. (2000) Infect Immun "Immunity to onchocerciasis: cells from putatively immune individuals produce enhanced levels of interleukin-5, gamma interferon, and granulocyte-macrophage colony-stimulating factor in response to Onchocerca volvulus larval and male worm antigens."

Lustigman S, Simonek SC, Bennett KE, Tierney TJ, McCarthy MC, Enyong PA, Turaga PS, Moukatte DW

[Infect Immun, 2000]

Antigen-specific interleukin-5 (IL-5), gamma interferon (IFN-gamma), and granulocyte-macrophage colony-stimulating factor (GM-CSF) responses in individuals living in an area of hyperendemicity for onchocerciasis in Cameroon were examined. The responses against antigens prepared from Onchocerca volvulus third-stage larvae (L3), molting L3 (mL3), and crude extract from adult males (M-OvAg) were compared to the responses against antigens from adult female worms and skin microfilariae. Cytokine responses for the putatively immune individuals (PI) and the infected individuals (INF) were compared. A differential cytokine profile of IL-5 (Th2 phenotype) and IFN-gamma (Th1 phenotype) was found in these individuals in response to the antigens. In both the PI and the INF, Th2 responses against all the antigens tested were dominant. However, in the PI group as a whole, there was an enhanced Th2 response against the larval antigens and the adult male and adult female antigens, and a Th1 response in a subgroup of the PI (27 to 54.5%) against L3, mL3, and M-OvAg antigens was present. While the PI produced significantly higher levels of GM-CSF against L3, mL3, and M-OvAg antigens than the INF, there was no difference in the GM-CSF responses of the groups against the other antigens. The present study indicated that, in comparison to the INF, the PI have distinct larva-specific and adult male-specific cytokine responses, thus supporting the premise that immunological studies of the PI would lead to the identification of immune mechanisms and the target genes that play a role in protective immunity.

Lieb JD et al. (1996) Science "DPY-26, a link between dosage compensation and meiotic chromosome segregation in the nematode."

Capowski EE, Meneely PM, Lieb JD, Meyer BJ

[Science, 1996]

The DPY-26 protein is required in the nematode Caenorhabditis elegans for X-chromosome dosage compensation as well as for proper meiotic chromosome segregation. DPY-26 was shown to mediate both processes through its association with chromosomes. In somatic cells, DPY-26 associates specifically with hermaphrodite X chromosomes to reduce their transcript levels. In germ cells, DPY-26 associates with all meiotic chromosomes to mediate its role in chromosome segregation. The X-specific localization of DPY-26 requires two dosage compensation proteins (DPY-27 and DPY-30) and two proteins that coordinately control both sex determination and dosage compensation (SDC-2 and SDC-3).AD - Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.FAU - Lieb, J DAU - Lieb JDFAU - Capowski, E EAU - Capowski EEFAU - Meneely, PAU - Meneely PFAU - Meyer, B JAU - Meyer BJLA - engSI - GENBANK/U43562SI - GENBANK/Z70680ID - GM30702/GM/NIGMSID - HD24324/HD/NICHDID - T32 GM07127/GM/NIGMSPT - Journal ArticleCY - UNITED STATESTA - ScienceJID - 0404511RN - 0 (Carrier Proteins)RN - 0 (DPY-27 protein)RN - 0 (Helminth Proteins)RN - 0 (Nuclear Proteins)SB - IM

Bailey S et al. (2002) Structure "The crystal structure of diadenosine tetraphosphate hydrolase from Caenorhabditis elegans in free and binary complex forms."

Bailey S, Baker PJ, Abdelghany HM, Blackburn GM, Rafferty JB, Sedelnikova SE, McLennan AG

[Structure, 2002]

The crystal structure of C. elegans Ap(4)A hydrolase has been determined for the free enzyme and a binary complex at 2.0 Angstrom. and 1.8 Angstrom, respectively. Ap(4)A hydrolase has a key role in regulating the intracellular Ap(4)A levels and hence potentially the cellular response to metabolic stress and/or differentiation and apoptosis via the Ap(3)A/Ap(4)A ratio. The structures reveal that the enzyme has the mixed alpha/beta fold of the Nudix family and also show how the enzyme binds and locates its substrate with respect to the catalytic machinery of the Nudix motif. These results suggest how the enzyme can catalyze the hydrolysis of a range of related dinucleoside tetraphosphate, but not triphosphate, compounds through precise orientation of key elements of the substrate.

Miller MA et al. (2001) Science "A sperm cytoskeletal protein that signals oocyte meiotic maturation and ovulation."

Schedl TB, Kosinski ME, Miller MA, Lee MH, Greenstein D, Caprioli RM, Nguyen VQ

[Science, 2001]

Caenorhabditis elegans oocytes, like those of most animals, arrest during meiotic prophase. Sperm promote the resumption of meiosis (maturation) and contraction of smooth muscle-like gonadal sheath cells, which are required for ovulation. We show that the major sperm cytoskeletal protein (MSP) is a bipartite signal for oocyte maturation and sheath contraction. MSP also functions in sperm locomotion, playing a role analogous to actin. Thus, during evolution, MSP has acquired extracellular signaling and intracellular cytoskeletal functions for reproduction. Proteins with MSP-like domains are found in plants, fungi, and other animals, suggesting that related signaling functions may exist in other phyla.AD - Department of Cell Biology, Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.FAU - Miller, M AAU - Miller MAFAU - Nguyen, V QAU - Nguyen VQFAU - Lee, M HAU - Lee MHFAU - Kosinski, MAU - Kosinski MFAU - Schedl, TAU - Schedl TFAU - Caprioli, R MAU - Caprioli RMFAU - Greenstein, DAU - Greenstein DLA - engID - CA09592/CA/NCIID - GM57173/GM/NIGMSID - GM58008/GM/NIGMSID - HD07043/HD/NICHDID - HD25614/HD/NICHDPT - Journal ArticleCY - United StatesTA - ScienceJID - 0404511RN - 0 (Carrier Proteins)RN - 0 (Helminth Proteins)RN - 0 (MAP Kinase Signaling System)RN - 0 (Membrane Proteins)RN - 0 (Recombinant Proteins)RN - 0 (VAP-33 protein)RN - 0 (major sperm protein, nematode)RN - EC 2.7.1.- (Mitogen-Activated Protein Kinases)SB - IM

Vassilieva LL et al. (1999) Genetics "The rate of spontaneous mutation for life-history traits in Caenorhabditis elegans."

Vassilieva LL, Lynch M

[Genetics, 1999]

Spontaneous mutations were accumulated in 100 replicate lines of Caenorhabditis elegans over a period of approximately 50 generations. Periodic assays of these lines and comparison to a frozen control suggest that the deleterious mutation rate for typical life-history characters in this species is at least 0.05 per diploid genome per generation, with the average mutational effect on the order of 14% or less in the homozygous state and the average mutational heritability approximately 0.0034. While the average mutation rate per character and the average mutational heritability for this species are somewhat lower than previous estimates for Drosophila, these differences can be reconciled to a large extent when the biological differences between these species are taken into consideration.AD - Department of Biology, University of Oregon, Eugene, Oregon 97403, USA.larissa@darkwing.uoregon.eduFAU - Vassilieva, L LAU - Vassilieva LLFAU - Lynch, MAU - Lynch MLA - engID - RO1-GM36827/GM/NIGMSPT - Journal ArticleCY - UNITED STATESTA - GeneticsJID - 0374636SB - IM