-
[
Nematologica,
1978]
A technique to axenize cultures of Caenorhabditis elegans on a large scale is described. This procedure has enabled the isolation of eggs of C. elegans in quantities sufficient to perform biochemical tests. Adults from monoxenic cultures were used to isolate eggs. When egg-bearing worms were suspended for 2-3 hr at 25C n an alkaline (0.4 M) solution of NaOH, the worm cuticle was partially digested, releasing free eggs. The high alkalinity rendered the eggs bacteria-free. Eggs were then isolated from a linear sucrose gradient. Eggs from the least dense band (1.13 g/cm3) hatched within 10-13 hr when resuspended in a liquid medium and yielded a synchronous culture. The hatchability of these eggs ranged from 20-35%. Inhibitory effects of 5-fluorodeoxyuridine and hydroxyurea on freshly hatched (L1 stage) worms are described. Levels of isocitrate lyase were determined in
-
[
Anal Biochem,
1976]
An ordinary spectrophotometer was used to study growth rates and increases in population size of nematodes by optical density measurements of nematodes suspended in 30-40% sucrose (w/v) solutions. The sucrose solution retarded the movement of nematodes in suspension and thereby decreased the fluctuations normally observed in optical density. This method was effectively used to study growth rates and increases in population numbers of a free-living nematode, Caenorhabditis elegans. This procedure was also used to quantitate Ascaris lumbricoides eggs in a given sample. The limitations of this method when employed for establishing total nematode counts in a growing culture by direct spectrophotometric readings are
-
[
Arch Biochem Biophys,
1977]
Biochemical evidence is presented suggesting the particulate nature of some of the glyoxylate cycle enzymes in the free-living nematode Caenorhabditis elegans. A crude homogenate of freshly grown nematodes was prepared by gentle grinding. Isopycnic sucrose gradient centrifugation of the supernatant fraction obtained by low-speed centrifugation yielded four protein bands. The glyoxylate cycle enzymes, isocitrate lyase and malate synthase, appeared in the lowermost band at a density of 1.25 g/cm3, while the mitochondrial enzymes, fumarase and NADH oxidase, equilibrated at a density of 1.18 g/cm3. The glyoxylate cycle and the mitochondrial enzymes were released differentially from the particulate fraction either by sonic treatment or by treatment with 0.1% Triton X-100. The specific activities of isocitrate lyase and malate synthase in the supernatant fraction obtained after a sonic treatment of the particulate fraction were always higher than those observed in the parent fraction.
-
[
Exp Parasitol,
1978]
The largest forms of isocitrate lyase from Caenorhabditis elegans and Ascaris suum of 543,000 and 549,000 daltons, respectively, can be purified from three- to five-fold in excellent yield by pelleting from extracts at 160,000g for 4 hr. Isocitrate lyase in the pellet is much more stable toward proteolysis. Itaconate which both inhibits isocitrate lyase and suppresses the level of this enzyme in bacteria inhibits the partially purified isocitrate lyase from both C. elegans and A. suum. The inhibition is noncompetitive with respect to D(s)-isocitrate at one itaconate concentration. The Ki values at 30C, pH 7.7, are 19 and 7.3 uM for the enzyme from C. elegans and A. suum, respectively. Itaconate inhibits the growth of C. elegans in random axenic as well as monoxenic cultures. At a concentration of 10 mM, itaconate is more effective in the inhibition of random axenic cultures than is oxalate, maleate, or succinate. At 60 mM itaconate, reproduction of C. elegans larvae is completely abolished.
-
[
Exp Parasitol,
1978]
It is well known that proteolysis often occurs after rupture of metazoan cells. Thus proteins isolated from extracts may not be representative of their native cellular counterparts. In the present research, extensive proteolysis was observed in crude extracts of the free-living soil nematode Caenorhabditis elegans and the parasitic nematode Ascaris suum. Phenylmethylsulfonyl fluoride (PMSF) reduced the loss in activity of isocitrate lyase (EC 4.1.3.1), fumarase (EC 4.2.1.2), and citrate synthase (EC 4.1.3.7) in extracts of C. elegans but had little or no effect upon loss of malate synthase (EC 4.1.3.2). Catalase (EC 1.11.1.6) was stable. The loss of isocitrate lyase and citrate synthase was less pronounced in extracts of 22-day-old embryos of A. suum. Catalase decayed in these extracts. The addition of PMSF reduced the loss in all three of these activities. Fumarase was stable. The number of active fragments of isocitrate lyase recovered after filtration on Sephadex G-200 increased with the length of storage of crude extracts in the absence of PMSF at 4C. Even in the presence of PMSF five activity peaks were observed after storage of extracts of C. elegans at 4C for 72 hr. The molecular weights of active species ranged between 549,000 and 128,000 for isocitrate lyase in extracts of either C. elegans or A. suum. The 549,000- and 214,000-dalton species of isocitrate lyase from A. suum were much more labile at 50C than the 543,000- and
-
[
Biochem Biophys Res Commun,
1999]
Mammalian thioredoxin reductases contain a TGA-encoded C-terminal penultimate selenocysteine (Sec) residue, and show little homology to bacterial, yeast, and plant thioredoxin reductases. Here we show that the nematode, Caenorhabditis elegans, contains two homologs related to the mammalian thioredoxin reductase family. The gene for one of these homologs contains a cysteine codon in place of TGA, and its product, designated TR-S, was previously suggested to function as thioredoxin reductase. The other gene contains TGA and its product is designated TR-Se. This Sec-containing thioredoxin reductase lacks a canonical Sec insertion sequence element in the 3'-untranslated area of the gene. TR-Se shows greater sequence similarity to mammalian thioredoxin reductase isozymes TR1 and TR2, whereas TR-S is more similar to TR3. TR-Se was identified as a thioredoxin reductase selenoprotein by labeling C. elegans with 75Se and characterizing the resulting 75Se-labeled protein by affinity and other column chromatography and gel-electrophoresis. TR-Se was expressed in Escherichia coli as a selenoprotein when a bacterial SECIS element was introduced downstream of the Sec TGA codon. The data show that TR-Se is the major naturally occurring selenoprotein in C. elegans, and suggest an important role for selenium and the thioredoxin system in this organism.
-
Shimono K, Honda N, Hasegawa T, Takahashi M, Hashimoto N, Sudo Y, Hayashi S, Mizutani K, Miyauchi S, Yamamoto M, Takagi S, Yamashita K, Tsukamoto T, Murata T
[
J Biol Chem,
2016]
Thermophilic rhodopsin (TR) is a photoreceptor protein with an extremely high thermal stability and the first characterized light-driven electrogenic proton pump derived from the extreme thermophile Thermus thermophilus JL-18. In this study, we confirmed its high thermal stability compared with other microbial rhodopsins and also report the potential availability of TR for optogenetics as a light-induced neural silencer. The x-ray crystal structure of TR revealed that its overall structure is quite similar to that of xanthorhodopsin, including the presence of a putative binding site for a carotenoid antenna; but several distinct structural characteristics of TR, including a decreased surface charge and a larger number of hydrophobic residues and aromatic-aromatic interactions, were also clarified. Based on the crystal structure, the structural changes of TR upon thermal stimulation were investigated by molecular dynamics simulations. The simulations revealed the presence of a thermally induced structural substate in which an increase of hydrophobic interactions in the extracellular domain, the movement of extracellular domains, the formation of a hydrogen bond, and the tilting of transmembrane helices were observed. From the computational and mutational analysis, we propose that an extracellular LPGG motif between helices F and G plays an important role in the thermal stability, acting as a "thermal sensor." These findings will be valuable for understanding retinal proteins with regard to high protein stability and high optogenetic performance.
-
[
Nematologica,
1980]
Biochemical studies of the free-living nematode C. elegans require large numbers grown axenically and synchronously. Patel & MacFadden developed a procedure using alkali at 25C to axenize cultures of C. elegans after which eggs were separated into three bands in a sucrose gradient, one of which contained eggs that hatched in 10-13 hrs yielding a synchronous culture. We now report an improvement which is faster, does not require density-gradient sedimentation and markedly increases hatchability.
-
[
Biophys J,
2019]
UNCoordinated-6 (UNC-6) was the first member of the netrin family to be discovered in Caenorhabditis elegans. With homology to human netrin-1, it is a key signaling molecule involved in directing axon migration in nematodes. Similar to netrin-1, UNC-6 interacts with multiple receptors (UNC-5 and UNC-40, specifically) to guide axon migration in development. As a result of the distinct evolutionary path of UNC-6 compared to vertebrate netrins, we decided to employ an integrated approach to study its solution behavior and compare it to the high-resolution structure we previously published on vertebrate netrins. Dynamic light scattering and analytical ultracentrifugation on UNC-6 (with and without its C-domain) solubilized in a low-ionic strength buffer suggested that UNC-6 forms high-order oligomers. An increase in the buffer ionic strength resulted in a more homogeneous preparation of UNC-6, that was used for subsequent solution x-ray scattering experiments. Our biophysical analysis of UNC-6 C solubilized in a high-ionic strength buffer suggested that it maintains a similar head-to-stalk arrangement as netrins -1 and -4. This phenomenon is thought to play a role in the signaling behavior of UNC-6 and its ability to move throughout the extracellular matrix.
-
[
Biochemistry,
2007]
High-molecular weight thioredoxin reductases (TRs) catalyze the reduction of the redox-active disulfide bond of thioredoxin, but an important difference in the TR family is the sequence of the C-terminal redox-active tetrapeptide that interacts directly with thioredoxin, especially the presence or absence of a selenocysteine (Sec) residue in this tetrapeptide. In this study, we have employed protein engineering techniques to investigate the C-terminal redox-active tetrapeptides of three different TRs: mouse mitochondrial TR (mTR3), Drosophila melanogaster TR (DmTR), and the mitochondrial TR from Caenorhabditis elegans (CeTR2), which have C-terminal tetrapeptide sequences of Gly-Cys-Sec-Gly, Ser-Cys-Cys-Ser, and Gly-Cys-Cys-Gly, respectively. Three different types of mutations and chemical modifications were performed in this study: insertion of alanine residues between the cysteine residues of the Cys-Cys or Cys-Sec dyads, modification of the charge at the C-terminus, and altering the position of the Sec residue in the mammalian enzyme. The results show that mTR3 is quite accommodating to insertion of alanine residues into the Cys-Sec dyad, with only a 4-6-fold drop in catalytic activity. In contrast, the activity of both DmTR and CeTR2 was reduced 100-300-fold when alanine residues were inserted into the Cys-Cys dyad. We have tested the importance of a salt bridge between the C-terminus and a basic residue that was proposed for orienting the Cys-Sec dyad of mTR3 for proper catalytic position by changing the C-terminal carboxylate to a carboxamide. The result is an enzyme with twice the activity as the wild-type mammalian enzyme. A similar result was achieved when the C-terminal carboxylate of DmTR was converted to a hydroxamic acid or a thiocarboxylate. Last, reversing the positions of the Cys and Sec residues in the catalytic dyad resulted in a 100-fold loss of catalytic activity. Taken together, the results support our previous model of Sec as the leaving group during reduction of the C-terminus during the catalytic cycle.