Complicated behavior of G-quadruplexes and evaluating G-quadruplexes' ligands in various systems mimicking cellular circumstance

Environments surrounding G-rich sequences remarkably affect the conformations of these structures. A proper evaluation system mimicking the crowded environment in a cell with macromolecules should be developed to perform structural and functional studies on G-quadruplexes. In this study, the topology and stability of a G-quadruplex formed by human telomeric repeat sequences were investigated in a macromolecule-crowded environment created by polyethylene glycol 200 (PEG200), tumor cell extract, and Xenopus laevis egg extract. The interactions between small molecules and telomeric G-quadruplexes were also evaluated in the different systems. The results suggested that the actual behavior of G-quadruplex structures in cells extract is quite different from that in the PEG crowding system, and proteins or other factors in extracts might play a very important role in G-quadruplex structures.     

Bufo japonicus japonicus and Xenopus laevis laevis egg jellies contain structurally related antigens and cortical granule lectin ligands

The antigenic relationship of the egg jelly coat glycoproteins from Bufo japonicus japonicus and Xenopus laevis laevis was investigated using agar double diffusion methods. The presence of ligands in the jelly coats for the cortical granule lectin from X.l. laevis eggs was also investigated. Anti-jelly serum for both anuran species crossreacted with the jelly coat from the other species with precipitin patterns of identity. Each egg jelly coat of both species contained two ligands for the cortical granule lectin. Although the ligands in the two different jelly coats appeared to react with the lectin in a pattern of identity, the species ligands were antigenically distinguishable using anti-Xenopus jelly serum. The observations that the two anuran egg jelly coats were antigenically related and that they both contained ligands for the X.l. laevis cortical granule lectin was interpreted in terms of fertilization mechanisms in the two different species. In addition, these observations bring into question the currently accepted phylogenetic relationship of B.j. japonicus and X.l. laevis.     

Characterization of two xenopus somatic 5S DNAs and one minor oocyte-specific 5S DNA

The somatic 5S DNA from X. borealis (Xbs 5S DNA) and X. laevis (Xis 5S DNA) and a minor oocyte-specific 5S DNA from X. laevis (Xit 5S DNA) have been purified, and individual repeating units have been cloned and sequenced. The two somatic 5S DNAs differ from the major oocyte 5S DNAs in having GC-rich spacers, homogeneous repeat lengths and no "pseudogenes." The somatic 5S DNAs from the two species have similar spacer sequences with differences due to single base changes and insertions/deletions. The spacer of the minor oocyte-specific 5S DNA (Xit) has the AT-rich sequence characteristic of the major oocyte 5S DNAs from X. laevis and X. borealis, and contains one duplication that has diverged approximately 40%. Like the somatic 5S DNAs, Xit 5S DNA has a homogeneous length repeat and a unique nucleotide sequence in its spacer. The presence of variable-length spacer regions in a multigene family correlates with variables numbers of a simple sequence in the spacer regions.     

Protein folding by the effects of macromolecular crowding

Unfolded states of ribonuclease A were used to investigate the effects of macromolecular crowding on macromolecular compactness and protein folding. The extent of protein folding and compactness were measured by circular dichroism spectroscopy, fluorescence correlation spectroscopy, and NMR spectroscopy in the presence of polyethylene glycol (PEG) or Ficoll as the crowding agent. The unfolded state of RNase A in a 2.4 M urea solution at pH 3.0 became native in conformation and compactness by the addition of 35% PEG 20000 or Ficoll 70. In addition, the effects of macromolecular crowding on inert macromolecule compactness were investigated by fluorescence correlation spectroscopy using Fluorescence-labeled PEG as a test macromolecule. The size of Fluorescence-labeled PEG decreased remarkably with an increase in the concentration of PEG 20000 or Ficoll 70. These results show that macromolecules are favored compact conformations in the presence of a high concentration of macromolecules and indicate the importance of a crowded environment for the folding and stabilization of globular proteins. Furthermore, the magnitude of the effects on macromolecular crowding by the different sizes of background molecules was investigated. RNase A and Fluorescence-labeled PEG did not become compact, and had folded conformation by the addition of PEG 200. The effect of the chemical potential on the compaction of a test molecule in relation to the relative sizes of the test and background molecules is also discussed.     

Xenopus laevis egg jelly contains small proteins that are essential to fertilization.

The eggs of Xenopus laevis are surrounded by investment layers of egg jelly that interact with the sperm immediately prior to fertilization. Components of these egg jelly layers are necessary for the fertilization of the egg by incoming sperm. Eggs which are stripped of their jelly layers are refractile to fertilization by sperm, but the addition of solubilized jelly promotes fertilization. We have shown previously that the egg jelly layers are composed of a fibrous network of glycoconjugates which loosely hold smaller diffusible components. Extracts of these diffusible components were prepared by incubation of freshly ovulated eggs in high-salt buffers for 12 h at 4 degrees C. This diffusible component extract, when incubated with sperm, promoted the sperm's ability to fertilize dejellied eggs in a dose-dependent manner. In contrast, the high-molecular-weight "structural" glycoconjugates of jelly that remain after extraction of the diffusible components did not increase fertilization efficiency of dejellied eggs nor did nonspecific proteins, carbohydrate polymers, or organic polymers. The diffusible components, analyzed by SDS-PAGE, consisted of a mixture of proteins from 4 to 180 kDa. The protein responsible for fertilization rescue appeared to be <50 kDa and appeared to self-aggregate or to bind to larger proteins. This protein component was required during sperm binding to the egg, its action required an intact egg vitelline envelope, and its action was independent of large soluble polymers such as Ficoll.     

DNA ligase I from Xenopus laevis eggs.

We have purified the major DNA ligase from Xenopus laevis eggs and raised antibodies against it. Estimates from SDS PAGE indicate that this DNA ligase is a 180 kDa protein. This enzyme is similar to the mammalian type I DNA ligase which is presumed to be involved in DNA replication. We have also analysed DNA ligase activity during X. laevis early development. Unfertilized eggs contain the highest level of activity reflecting the requirement for a large amount of DNA replicative enzymes for the period of intense replication following fertilization. In contrast with previous studies on the amphibians axolotl and Pleurodeles, the major DNA ligase activity detected during X. laevis early development is catalysed by a single enzyme: DNA ligase I. And the presence of this DNA ligase I in Xenopus egg before fertilization clearly demonstrates that the exclusion process of two forms of DNA ligase does not occur during X. laevis early development.     

Cross-fertilization and structural comparison of egg extracellular matrix glycoproteins from Xenopus laevis and Xenopus tropicalis

While the anuran amphibian Xenopus laevis is a widely used vertebrate model system, it is not optimal for genetic manipulations due to its tetraploid genome and long generation time. A current alternative amphibian model system, Xenopus tropicalis, has the advantages of a diploid genome and a much shorter generation time. We undertook a comparative investigation of X. tropicalis egg extracellular matrix glycoproteins in relation to those already characterized in X. laevis. Fertilization methods and isolation of egg extracellular molecules were directly transferable from X. laevis to X. tropicalis. Cross-fertilizations were successful in both directions, indicating similar molecules involved in sperm-egg interactions. Egg envelopes analyzed by SDS-PAGE were found to have almost identical gel patterns, whereas jelly component profiles were similar only for the larger macromolecules (>90 kDa). The cDNA sequences for egg envelope glycoproteins ZPA, ZPB, ZPC, ZPD and ZPAX, and also egg cortical granule lectin involved in the block to polyspermy, were cloned for X. tropicalis and showed a consistent approximately 85% amino acid identity to the X. laevis sequences. Thus, homologous egg extracellular matrix molecules perform the same functions, and the molecular and cellular mechanisms of fertilization in these two species are probably equivalent.     

Mesoderm formation in Eleutherodactylus coqui: body patterning in a frog with a large egg.

The direct developing frog, Eleutherodactylus coqui, develops from a large egg (diameter 3.5 mm). To investigate the effect of egg size on germ-layer formation, we studied mesoderm formation in E. coqui and compared it to that of Xenopus laevis (diameter 1.3 mm). First, we identified the position of prospective mesoderm in the 16-cell E. coqui embryo by cell-lineage tracing. Although the animal blastomeres are small, they form most of the blastocoel roof and make extensive contributions to some mesodermal tissues. Second, we performed recombinant analysis with X. laevis animal caps to define the distribution of mesoderm-inducing activity. Mesoderm-inducing activity in E. coqui was restricted around the marginal zone with strong activity in the superficial cells. Neither the vegetal pole nor the blastocoel floor had activity, although these same regions from X. laevis induced mesoderm. Third, we cloned Ecbra, a homologue of Xbra, an early mesoderm marker in X. laevis. Ecbra was expressed in the marginal ring close to the surface, similar to X. laevis, but E. coqui had weaker expression on the dorsal side. Our results suggest that mesoderm formation is shifted more animally and superficially in E. coqui compared to X. laevis.     

A comparison of four different conformations adopted by human telomeric G‐quadruplex using computer simulations

The telomeric G‐quadruplexes for their unique structural features are considered as potential anticancer drug targets. These, however, exhibit structural polymorphism as different topology types for the intra‐molecular G‐quadruplexes from human telomeric G‐rich sequences have been reported based on NMR spectroscopy and X‐ray crystallography. These techniques provide detailed atomic‐level information about the molecule but relative conformational stability of the different topologies remains unsolved. Therefore, to understand the conformational preference, we have carried out quantum chemical calculations on G‐quartets; used all‐atom molecular dynamics (MD) simulations and steered molecular dynamics (SMD) simulations to characterize the four human telomeric G‐quadruplex topologies based on its G‐tetrad core‐types, viz., parallel, anti‐parallel, mixed‐(3 + 1)‐form1 and mixed‐(3 + 1)‐form2. We have also studied a non‐telomeric sequence along with these telomeric forms giving a comparison between the two G‐rich forms. The structural properties such as base pairing, stacking geometry and backbone conformations have been analyzed. The quantum calculations indicate that presence of a sodium ion inside the G‐tetrad plane or two potassium ions on both sides of the plane give it an overall planarity which is much needed for good stacking to form a helix. MD simulations indicate that capping of the G‐tetrad core by the TTA loops keep the terminal guanine bases away from water. The SMD simulations along with equilibrium MD studies indicate that the parallel and non‐telomeric forms are comparatively less stable. We could come to the conclusion that the anti‐parallel form and also the mixed‐(3 + 1)‐form1 topology are most likely to represent the major conformation., 2016. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 83–99, 2016     

Localization of repetitive DNA sequences on in vitro Xenopus laevis chromosomes by primed in situ labeling (PRINS)

Xenopus laevis is an important reference model organism used in many vertebrate studies. Gene mapping in X. laevis, in comparison to other reference organisms, is in its early stages. Few studies have been conducted to localize DNA sequences on X. laevis chromosomes. Primed in situ labeling (PRINS) is a recently developed innovative tool that has been used to locate specific DNA sequences in various organisms. PRINS has been reported to have increased sensitivity compared to other in situ hybridization techniques. In the present study, PRINS was first used to label the location of telomeres at the ends of in vitro X. laevis chromosomes. The terminal location was as expected from in vivo reports, however, the overall amount seemed to decrease in the in vitro chromosomes. Once the PRINS technique was optimized, this technique was used to determine the chromosomal location of the satellite 1 repetitive sequence, which is an important sequence in X. laevis development. The sequence was observed on the interstitial regions of the majority of the chromosomes similar to the in vivo locations reported. In contrast to the telomeric sequence, the amount of sequence appeared to increase in the satellite 1 sequence. PRINS was found to be useful in the localization of repetitive DNA sequences in the X. laevis genome.     

Parallel microtubules and other conserved elements of dorsal axial specification in the direct developing frog, <Emphasis Type="Italic">Eleutherodactylus coqui</Emphasis>

Specification of the dorsal axis in commonly studied frogs, such as Xenopus laevis and Rana pipiens, depends on a microtubule-mediated movement of cytoplasm in the fertilized egg. The Puerto Rican tree frog, Eleutherodactylus coqui, has an egg that is twenty times the volume of that of X. laevis, raising the question as to whether the mechanism of dorsal axial specification is conserved in these large eggs. Fertilized eggs of E. coqui develop a transient array of parallel microtubules, similar to other frogs, but proportionately larger. The array persists after first cleavage, longer than in other frogs, and is gone by the third cleavage. Correlated with the longer life of the parallel microtubules, both 2- and 8-cell E. coqui embryos remain sensitive to gravity-mediated axial specification, a sensitivity lost in X. laevis before the 2-cell stage. Activation of the Wnt/beta-catenin pathway by injected Xwnt8 RNA causes axial formation as in X. laevis. The results indicate that elements of dorsal axial specification are conserved in E. coqui, but they occur later compared to in X. laevis.     

Viscoelastic properties of plasticized methylcellulose and chemically crosslinked methylcellulose

Films of methylcellulose (MC), poly(ethylene glycol)400 (PEG400) plasticized MC, and MC gels (MC crosslinked with glutaraldehyde (GA)) were prepared by casting from aqueous solutions. The swelling test has shown that the MC gels were insoluble in water and that their crosslinking density increased with increasing GA and HCl concentrations. The effect of the addition of PEG400 or GA to MC was investigated through dynamic mechanical analysis (DMA). The DMA analysis of PEG400/MC blends has shown that PEG400 was compatible with MC and was an effective plasticizer since the curves of tan δ against temperature exhibited single peaks (corresponding to a single glass transition temperature), which were displaced to lower values with increasing PEG400 content. The thermogravimetric analysis (TGA) indicated that the thermal stability of MC was not affected by the chemical crosslinking. The tensile strength was slightly increased through crosslinking while the elongation was slightly decreased. The presence of moisture in MC hydrogels decreased the tensile strength and enhanced the elongation while the addition of PEG400 decreased the tensile strength but sharply increased the elongation.     

Purification and multimer formation of allurin, a sperm chemoattractant from Xenopus laevis egg jelly

Allurin, a sperm chemoattractant isolated from Xenopus laevis egg jelly, can be purified in one step from an extract of diffusible jelly proteins ("egg water") using a FPLC or HPLC anion exchange column and a multi-step NaCl gradient. Allurin homomultimers were detected by Western blotting with antibodies prepared against the purified protein or peptides within the protein. Allurin multimers were stable and resisted dissociation by SDS and beta-mercaptoethanol. Alkylation of allurin provided evidence for two free sulfhydryl groups but did not eliminate multimer formation, suggesting that intermolecular disulfide bond formation is not required for allurin aggregation. Concentration of egg water was accompanied by a reduction of chemoattractant activity that could not be fully accounted for by homomultimer formation. Rather, the presence of a multiphasic dose-activity curve upon partial purification and formation of hetero-allurin complexes during concentration suggested that egg water may contain allurin-binding proteins that reduce multimer formation and activity.     

Native yeast telomeres are sufficient to stabilize linear DNA in Xenopus laevis oocytes.

We have constructed a linear plasmid in yeast containing the entire bovine papillomavirus genome and tested its physical stability following microinjection into stage VI oocytes of Xenopus laevis. Our results show that unmodified telomeres, in contrast to the yeast-passaged telomeres, drastically affect the stability of the injected linear plasmid. Plasmids carrying unmodified Tetrahymena thermophila telomeric sequences are rapidly degraded in oocytes. When these plasmids are passed through yeast, the telomere ends become modified by the addition of yeast telomeric sequences. These plasmids are stably maintained in X. laevis oocytes, demonstrating that yeast-modified telomeres are sufficient to prevent linear DNA degradation.     

Electrically induced fusion of mammalian cells in the presence of polyethylene glycol

Chinese Hamster Ovary (CHO) cells were fused by subjecting cell suspensions to an exponentially decaying electric pulse in the presence of polyethylene glycol (PEG), Dextran or Ficoll. PEG (MW 1,000, 3,350, 8,000, 10,000 and 18,500), Dextran (MW 71,200) and Ficoll (MW 400,000) were added to the pulsing medium. A single exponential electric pulse with peak field strength of 4 kV/cm, and a half-time of 0.72 msec was used. The combination of two techniques, PEG-induced fusion and electrofusion, resulted in highly efficient fusion of CHO cells. Fusion yields (FY) at different concentrations of these polymers were measured using phase-contrast microscopy. FY was highly dependent on the concentration of PEG in media, while the presence of Dextran and Ficoll had no influence on fusion yield. PEG with MW 8,000 was found to be the most effective in causing cell aggregation, and to give the highest FY (40%). An optimal concentration for fusion was found for PEG of each molecular weight. Diluting cells suspended in higher concentrations of PEG to these optimal concentrations after the pulse application regained the optimal FY. It was concluded that PEG-induced prepulse aggregation and moderate cell swelling immediately after the pulse were important factors in achieving high fusion yields.This work is supported by a grant GM-30969 from the National Institutes of Health. Traveling fellowship to N.G.S. was supported from Foundation Cyrill and Methodius and grant N-189 from MCES of Bulgaria.     

Viability,cell division and microcallus formation of barley microspores in culture

Barley microspores were viable when cultured in a sugarless medium. Adding 2g of glucose to 1l of this medium resulted in a significant reduction in the frequency of viable microspores. The frequency of viable microspores was further reduced when 50g of cellobiose, glucose, maltose, melezitose, raffinose or sucrose were added to 1l of the culture medium containing 2g/l glucose. Adding 50g of melibiose, Ficoll, polyethylene glycol (PEG) or a combination 50g each of Ficoll and PEG to 1I of the medium containing 2g/l glucose had very little effect on the viability of the microspores.Up to 66% of the viable microspores were able to divide and many of these developed into microcalli in the basal medium complemented with melibiose, maltose, melezitose, raffinose, Ficoll, PEG or a combination of Ficoll with PEG. Sucrose, cellobiose and glucose added in large quantities inhibited cell division in microspores or destabilized the microspores and only very few of them developed into microcalli.The microcalli in the PEG, Ficoll, Ficoll-PEG and melibiose media were smaller in size than those grown in the melezitose, maltose and raffinose media. Sustained cell division and microcallus formation were observed in a medium with melibiose or maltose as sole source of sugars.Abbreviations 2.4-D 2,4-dichlorophenoxyacetic acid - NAA 1-Naphthaleneacetic acid - PEG Polyethylene glycol     

Mixed macromolecular crowding accelerates the refolding of rabbit muscle creatine kinase: implications for protein folding in physiological environments

The effects of four single macromolecular crowding agents, Ficoll 70, dextran 70, polyethylene glycol (PEG) 2000, and calf thymus DNA (CT DNA), and three mixed crowding agents containing both CT DNA and polysaccharide (or PEG 2000) on the refolding of guanidine hydrochloride-denatured rabbit muscle creatine kinase (MM-CK) have been examined by activity assay. When the total concentration of the mixed crowding agent is 100 g/l, in which the weight ratio of CT DNA to Ficoll 70 is 1:9, the refolding yield of MM-CK after refolding for 3 h under these conditions increases 23% compared with that in the presence of 10 g/l CT DNA, 18% compared with 100 g/l Ficoll 70, and 19% compared with that in the absence of crowding agents. A remarkable increase in the refolding yield of MM-CK by a mixed crowding agent containing CT DNA and dextran 70 (or PEG 2000) is also observed. Further folding kinetics analyses show that these three mixed crowding agents remarkably accelerate the refolding of MM-CK, compared with single crowding agents. Aggregation of MM-CK in the presence of any of the three mixed crowding agents is less serious than that in the presence of a single crowding agent at the same concentration but more serious than that in the absence of crowding agents. Both the refolding yield and the refolding rate of MM-CK in mixtures of these agents are increased relative to the individual agents by themselves, indicating that mixed macromolecular crowding agents are more favorable to MM-CK folding and can be used to reflect the physiological environment more accurately than single crowding agents.