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[
Proc Natl Acad Sci U S A,
1999]
Caenorhabditis elegans should soon be the first multicellular organism whose complete genomic sequence has been determined. This achievement provides a unique opportunity for a comprehensive assessment of the signal transduction molecules required for the existence of a multicellular animal. Although the worm C. elegans may not much resemble humans, the molecules that regulate signal transduction in these two organisms prove to be quite similar. We focus here on the content and diversity of protein kinases present in worms, together with an assessment of other classes of proteins that regulate protein phosphorylation. By systematic analysis of the 19,099 predicted C. elegans proteins, and thorough analysis of the finished and unfinished genomic sequences, we have identified 411 full length protein kinases and 21 partial kinase fragments. We also describe 82 additional proteins that are predicted to be structurally similar to conventional protein kinases even though they share minimal primary sequence identity. Finally, the richness of phosphorylation-dependent signaling pathways in worms is further supported with the identification of 185 protein phosphatases and 128 phosphoprotein-binding domains (SH2, PTB, STYX, SBF, 14-3-3, FHA, and WW) in the worm genome.
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[
J Cell Biochem,
2000]
With the availability of the nearly complete genomic sequence of C. elegans, the first multicellular organism to be sequenced, molecular biology has definitely entered the postgenomic era. Annotation of the genomic sequence, which refers to identifying the genes and other biologically relevant sections of the genome, is an important and nontrivial next step. A first-pass annotation will be necessarily incomplete but will drive further biological experiments, which in turn will help to annotate the genome better. Given the scale of the genome sequence analysis, it is clear that the annotation should be automated as much as possible without sacrificing the quality of analysis. In this work, we outline our approach to identifying the protein kinases of C. elegans from the genomic sequence. We describe new tools we have developed for analysis, management and visualization of genomic data. By developing modular and scalable solutions, this study has provided a framework for future analysis of the Drosophila and human genomes.
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[
Nanoscale,
2011]
Gd@C(82)(OH)(22), a water-soluble endohedral metallofullerene derivative, has been proven to possess significant antineoplastic activity in mice. Toxicity studies of the nanoparticle have shown some evidence of low or non toxicity in mice and cell models. Here we employed Caenorhabditis elegans (C. elegans) as a model organism to further evaluate the short- and long-term toxicity of Gd@C(82)(OH)(22) and possible behavior changes under normal and stress culture conditions. With treatment of Gd@C(82)(OH)(22) at 0.01, 0.1, 1.0 and 10 g ml(-1) within one generation (short-term), C. elegans showed no significant decrease in longevity or thermotolerance compared to the controls. Furthermore, when Gd@C(82)(OH)(22) treatment was extended up to six generations (long-term), non-toxic effects to the nematodes were found. In addition, data from body length measurement, feeding rate and egg-laying assays with short-term treatment demonstrated that the nanoparticles have no significant impact on the individual growth, feeding behavior and reproductive ability, respectively. In summary, this work has shown that Gd@C(82)(OH)(22) is tolerated well by worms and it has no apparent toxic effects on longevity, stress resistance, growth and behaviors that were observed in both adult and young worms. Our work lays the foundations for further developments of this anti-neoplastic agent for clinical applications.
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[
Trends in Biochemical Sciences,
2002]
Protein phosphorylation controls many cellular processes, especially those involved in intercellular communication and coordination of complex functions. To explore the evolution of protein phosphorylation, we compared the protein kinase complements ('kinomes') of budding yeast, worm and fly, with known human kinases. We classify kinases into putative orthologous groups with conserved functions and discuss kinase families and pathways that are unique, expanded or lost in each lineage. Fly and human share several kinase families involved in immunity, neurobiology, cell cycle and morphogenesis that are absent from worm, suggesting that these functions might have evolved after the divergence of nematodes from the main metazoan lineage.
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[
Biochim Biophys Acta Proteins Proteom,
2023]
Out of the 34 globins in Caenorhabditis elegans, GLB-33 is a putative globin-coupled transmembrane receptor with a yet unknown function. The globin domain (GD) contains a particularly hydrophobic haem pocket, that rapidly oxidizes to a low-spin hydroxide ligated haem state at physiological pH. Moreover, the GD has one of the fastest nitrite reductase activity ever reported for globins. Here, we use a combination of electronic circular dichroism, resonance Raman and electron paramagnetic resonance (EPR) spectroscopy with mass spectrometry to study the pH dependence of the ferric form of the recombinantly over-expressed GD in the presence and absence of nitrite. The competitive binding of nitrite and hydroxide is examined as well as nitrite-induced haem modifications at acidic pH. Comparison of the spectroscopic results with data from other haem proteins allows to deduce the important effect of Arg at position E10 in stabilization of exogenous ligands. Furthermore, continuous-wave and pulsed EPR indicate that ligation of nitrite occurs in a nitrito mode at pH&#
x202f;5.0 and above. At pH&#
x202f;4.0, an additional formation of a nitro-bound haem form is observed along with fast formation of a nitri-globin.
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Schoofs L, Desmet F, Moens L, Van Doorslaer S, Tilleman L, Braeckman BP, Helbo S, Hoogewijs D, Fago A, Germani F, Dewilde S, Berghmans H, De Henau S
[
J Biol Chem,
2015]
We report the structural and biochemical characterization of GLB-33, a putative neuropeptide receptor that is exclusively expressed in the nervous system of the nematode Caenorhabditis elegans. This unique chimeric protein is composed of a 7-transmembrane domain (7TM), GLB-33 7TM, typical of a G-protein-coupled receptor, and of a globin domain (GD), GLB-33 GD. Comprehensive sequence similarity searches in the genome of the parasitic nematode, Ascaris suum, revealed a chimeric protein that is similar to a Phe-Met-Arg-Phe-amide neuropeptide receptor. The three-dimensional structures of the separate domains of both species and of the full-length proteins were modeled. The 7TM domains of both proteins appeared very similar, but the globin domain of the A. suum receptor surprisingly seemed to lack several helices, suggesting a novel truncated globin fold. The globin domain of C. elegans GLB-33, however, was very similar to a genuine myoglobin-type molecule. Spectroscopic analysis of the recombinant GLB-33 GD showed that the heme is pentacoordinate when ferrous and in the hydroxide-ligated form when ferric, even at neutral pH. Flash-photolysis experiments showed overall fast biphasic CO rebinding kinetics. In its ferrous deoxy form, GLB-33 GD is capable of reversibly binding O2 with a very high affinity and of reducing nitrite to nitric oxide faster than other globins. Collectively, these properties suggest that the globin domain of GLB-33 may serve as a highly sensitive oxygen sensor and/or as a nitrite reductase. Both properties are potentially able to modulate the neuropeptide sensitivity of the neuronal transmembrane receptor.
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[
Cell,
2011]
Parkinson's disease (PD), an adult neurodegenerative disorder, has been clinically linked to the lysosomal storage disorder Gaucher disease (GD), but the mechanistic connection is not known. Here, we show that functional loss of GD-linked glucocerebrosidase (GCase) in primary cultures or human iPS neurons compromises lysosomal protein degradation, causes accumulation of -synuclein (-syn), and results in neurotoxicity through aggregation-dependent mechanisms. Glucosylceramide (GlcCer), the GCase substrate, directly influenced amyloid formation of purified -syn by stabilizing soluble oligomeric intermediates. We further demonstrate that -syn inhibits the lysosomal activity of normal GCase in neurons and idiopathic PD brain, suggesting that GCase depletion contributes to the pathogenesis of sporadic synucleinopathies. These findings suggest that the bidirectional effect of -syn and GCase forms a positive feedback loop that may lead to a self-propagating disease. Therefore, improved targeting of GCase to lysosomes may represent a specific therapeutic approach for PD and other synucleinopathies.
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[
Bioinformatics,
2010]
MOTIVATION: Digital reconstruction of 3D neuron structures is an important step toward reverse engineering the wiring and functions of a brain. However, despite a number of existing studies, this task is still challenging, especially when a 3D microscopic image has low single-to-noise ratio and discontinued segments of neurite patterns. RESULTS: We developed a graph-augmented deformable model (GD) to reconstruct (trace) the 3D structure of a neuron when it has a broken structure and/or fuzzy boundary. We formulated a variational problem using the geodesic shortest path, which is defined as a combination of Euclidean distance, exponent of inverse intensity of pixels along the path and closeness to local centers of image intensity distribution. We solved it in two steps. We first used a shortest path graph algorithm to guarantee that we find the global optimal solution of this step. Then we optimized a discrete deformable curve model to achieve visually more satisfactory reconstructions. Within our framework, it is also easy to define an optional prior curve that reflects the domain knowledge of a user. We investigated the performance of our method using a number of challenging 3D neuronal image datasets of different model organisms including fruit fly, Caenorhabditis elegans, and mouse. In our experiments, the GD method outperformed several comparison methods in reconstruction accuracy, consistency, robustness and speed. We further used GD in two real applications, namely cataloging neurite morphology of fruit fly to build a 3D 'standard' digital neurite atlas, and estimating the synaptic bouton density along the axons for a mouse brain. AVAILABILITY: The software is provided as part of the V3D-Neuron 1.0 package freely available at
http://penglab.janelia.org/proj/v3d. -
Chen, Y., Onken, B., Cao, Y., Huang, Q., Chen, H., Driscoll, M., Xiao, S.
[
International Worm Meeting,
2013]
To identify potential pharmacological compounds that delay the progression of age-related degenerative changes and illness, we monitored the effects of six hydrolysable tannins with high antioxidant activities isolated from Eucalyptus leaves (Oenothein B (OEB), 1,2,3,4,6-penta-O-galloyl-b-D-glucose (PGG), Tellimagrandin I (T1), Tellimagrandin II(T2), Pedunculagin (Ped) and Gemin D (GD) ) on C. elegans lifespan at four different concentrations. We found that of the six, OEB and PGG extended lifespan in a dose-dependent manner and increased median lifespan by up to 22%. OEB significantly prolonged youthful locomotory ability. We also found that the survival curves of T1-treated animals at all tested concentrations were significantly increased, although median lifespan was not significantly improved. OEB, PGG and T1 did not significantly affect the age-associated physiological functions of reproduction, pharyngeal pumping rate, or age pigment accumulation. Animals treated with 40 mM Ped significantly extended median lifespan by 11%, but we did not observe any significant benefits at other Ped concentrations. T2 and GD did not cause significant lifespan extension at any tested concentration. To further determine how OEB and PGG prolong C. elegans lifespan, we investigated the genetic requirements for these benefits. Strikingly, we found that lifespan extension with OEB and PGG treatment was driven by the insulin signaling, dietary restriction, and mitochondrial function pathways, indicating that these compounds target multiple longevity mechanisms to promote lifespan. Together, our results demonstrate broad-based aging benefits with these botanical compounds, which may be exploited in novel therapies to promote healthy aging.
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[
Langmuir,
2014]
Three different sizes of Eu0.2Gd0.8PO4-H2O nanoparticles have been prepared to investigate the particle size influence on water proton relaxivity. Longitudinal relaxivity (
r1) values increase for smaller particles, reaching as high as
r1 = 6.13 mM(-1) s(-1) for a sample of 40 +/- 4 nm particles, which, with a ratio of transverse/longitudinal relaxivity,
r2/r1 = 1.27, are shown to be effective positive contrast agents. The correlation between relaxivity and the surface-to-volume ratio implies that access to surface Gd(3+) sites is the principal factor affecting relaxivity. On the other hand, although ionic molar relaxivity decreases for larger particles, the relaxivity per particle can be significantly greater. Gadolinium-based nanoparticles doped with fluorescent lanthanide elements have attracted attention for their dual-imaging abilities, combining magnetic resonance imaging (MRI) and fluorescence imaging agents. In both in vitro experiments with HeLa cells and in vivo experiments with C. elegans, strong red fluorescence is observed from Eu0.2Gd0.8PO4-H2O with high resolution, demonstrating the parallel use of the particles as fluorescence imaging agents.