Cell cycle-dependent mobility of Cdc45 determined in vivo by fluorescence correlation spectroscopy

Eukaryotic DNA replication is a dynamic process requiring the co-operation of specific replication proteins. We measured the mobility of eGFP-Cdc45 by Fluorescence Correlation Spectroscopy (FCS) in vivo in asynchronous cells and in cells synchronized at the G1/S transition and during S phase. Our data show that eGFP-Cdc45 mobility is faster in G1/S transition compared to S phase suggesting that Cdc45 is part of larger protein complex formed in S phase. Furthermore, the size of complexes containing Cdc45 was estimated in asynchronous, G1/S and S phase-synchronized cells using gel filtration chromatography; these findings complemented the in vivo FCS data. Analysis of the mobility of eGFP-Cdc45 and the size of complexes containing Cdc45 and eGFP-Cdc45 after UVC-mediated DNA damage revealed no significant changes in diffusion rates and complex sizes using FCS and gel filtration chromatography analyses. This suggests that after UV-damage, Cdc45 is still present in a large multi-protein complex and that its mobility within living cells is consistently similar following UVC-mediated DNA damage.     

Protein osmotic pressure and the state of water in frog myoplasm

We measured the osmotic pressure of diffusible myoplasmic proteins in frog (Rana temporaria) skeletal muscle fibers by using single Sephadex beads as osmometers and dialysis membranes as protein filters. The state of the myoplasmic water was probed by determining the osmotic coefficient of parvalbumin, a small, abundant diffusible protein distributed throughout the fluid myoplasm. Tiny sections of membrane (3.5- and 12-14-kDa cutoffs) were juxtaposed between the Sephadex beads and skinned semitendinosus muscle fibers under oil. After equilibration, the beads were removed and calibrated by comparing the diameter of each bead to its diameter measured in solutions containing 3-12% Dextran T500 (a long-chain polymer). The method was validated using 4% agarose cylinders loaded with bovine serum albumin (BSA) or parvalbumin. The measured osmotic pressures for 1.5 and 3.0 mM BSA were similar to those calculated by others. The mean osmotic pressure produced by the myoplasmic proteins was 9.7 mOsm (4 degrees C). The osmotic pressure attributable to parvalbumin was estimated to be 3.4 mOsm. The osmotic coefficient of the parvalbumin in fibers is approximately 3.7 mOsm mM(-1), i.e., roughly the same as obtained from parvalbumin-loaded agarose cylinders under comparable conditions, suggesting that the fluid interior of muscle resembles a simple salt solution as in a 4% agarose gel.     

The distribution and relation to the cytoskeleton of specific prosomal proteins in the oogenesis of the clawed toad]

Using immunoblotting and immunofluorescent microscopy, we showed the presence in Xenopus laevis oocytes of two prosomal proteins (27 and 31-33 kDa) and studied their distribution during oogenesis. In the ooplasm, both proteins are detected in prosomal clusters of various size. During previtellogenesis, prosomal proteins are diffusely distributed in the nucleoplasm and form evenly distributed clusters in the cytoplasm. During oocyte growth, prosomal proteins disappear from the nucleus and form animal-vegetal and cortical gradients in the cytoplasm. In the course of oocyte maturation prosomal clusters become smaller. After artificial activation of the egg, the dorso-ventral gradient of distribution of prosomal proteins is observed. Double immunohistochemical labeling revealed morphological association between prosomal clusters and fibril-like structures of the oocyte containing actin and myosin. The latter are then replaced by diffusely distributed actin and myosin. Thus, correlation is observed between localization of the acto-myosin complex of the oocyte and that of prosomal proteins.     

Gel-exclusion chromatography on S1000 sephacryl: Application to phospholipid vesicles

Sephacryl S1000 has an exclusion diameter of approximately 3000 Å and is thus an appropriate gel exclusion medium for size analysis and fractionation of phospholipid vesicles. Calibration is conveniently carried out using polystyrene beads of known diameter eluted with a detergent-containing buffer. Recovery of phospholipid vesicles of different sizes from S1000 presaturated with lipid is greater than 95%, and diameters obtained from a calibration curve using the polystyrene beads are in good agreement with those obtained by negative contrast electron microscopy.     

Evidence against electrophoresis as the principal mode of protein transport in vitellogenic ovarian follicles of Drosophila

Charged cell constituents in polytrophic insect follicles are thought to be transported in the nurse cell-oocyte syncytium by way of electrophoresis. This concept, proposed by Woodruff & Telfer (1980) was based on electrophysiological data and microinjection of heterologous proteins using Hyalophora follicles. By microinjecting fluorescently labelled acidic and basic proteins into the nurse cells or oocyte of vitellogenic Drosophila follicles, we failed to obtain evidence for charge-dependent migration of these molecules. We have also analyzed the proteins of nurse cells and oocyte on isoelectric focusing gels, by means of two-dimensional gel electrophoresis, and by ion exchange chromatography to see if basic or acidic proteins accumulate in vivo in nurse cells and oocyte, respectively. For the bulk of the follicular proteins we found no accumulation. Further evidence against an electrophoretic transport system in Drosophila was obtained by estimating the intracellular pH from the colour of indicator dyes microinjected into the follicles; the results indicate that the pH in the nurse cell cytoplasm is lower than that in the ooplasm. According to the model developed for Hyalophora, electrophoretic transport would be favoured by high pH in the nurse cell cytoplasm.     

Ribosomal-protein synthesis is not autogenously regulated at the translational level in Xenopus laevis

Whether ribosomal-protein synthesis in Xenopus laevis is autogenously controlled at the translational level as is known to occur in prokaryotes has been studied. For this purpose ribosomal (r) proteins were prepared from X. laevis ribosomal subunits and group fractionated by ion-exchange chromatography. They were then added to an in vitro translation system directed by an oocyte mRNA fraction which contains template activity for r proteins. The synthesized radioactive products were analyzed by 2D gel electrophoresis and compared with controls. Similarly in vivo experiments were performed by microinjection of the fractionated proteins into the cytoplasm of Xenopus oocytes followed by incubation with [35S]methionine for different times. In all the experiments no evident effect of r proteins on the translation of their own mRNA was observed.     

Distribution of prosome proteins and their relationship with the cytoskeleton in oogenesis of Xenopus laevis

The presence of prosome proteins (p25K and p27K) was shown and their distribution was studied in oogenesis of Xenopus laevis using immunoblotting and immunofluorescence. These proteins form numerous granular clusters of variable size all over the cell. At previteilogenic stages, the prosome antibodies homogeneously stain the oocyte nucleus and the evenly distributed relatively large clusters in the cytoplasm. As the oocyte grows, the pattern of distribution of the prosome proteins undergoes changes: animal-vegetal and cortical gradients appear in the cytoplasm. In the course of oocyte maturation the size of clusters diminishes. Artificial activation of the egg leads to a dorso-ventral gradient in distribution of the prosome proteins. In this way, specific localization of prosome proteins is first visualized during formation of the dorso-ventral polarity. Co-localization of prosome proteins and actin and myosin was found in the oocyte by double staining. Small clusters of prosomes dispersed in the cytoplasm acquire capability of movement (after artificial activation) due, in all likelihood, to persisting connection with the acto-myosin complex of the egg. © 1994 Wiley-Liss, Inc.     

Study of the translational diffusion of macromolecules in beads of gel chromatography by the FRAP method

We measured the translational diffusion of fractions of dextrans labelled with fluorescein isothiocyanate, in Sephadex gel beads permeated by aqueous solutions of these molecules. The molecular weights of these fractions were between 5400 and 200,000 and measurements of their diffusion coefficients inside a gel bead (D) and in the free solution (D0), were performed using the fluorescence recovery after photobleaching method (FRAP). We also determined the coefficient of partitioning (Kav) of these fractions between the gel and the free solvent, with a new microfluorimetric method. We found that, for Sephadex G-50, G-75, G-100, G-150 and G-200 gels, Kav varied with the Stokes radius (rs) of the dextran molecules, in agreement with the formula of Laurent and Killander (J. Chromatogr. 14 (1964) 317). For Sephadex G-100, G-150 and G-200 gels, D/D0 varied with rs, according to the theory of Ogston et al. (Proc. R. Soc. Lond. 333 (1973) 297). In addition, these theories predict a relation linking D/D0 to Kav which was well verified. Our work is the first systematic study of the translational diffusion of macromolecules in a chromatography gel. These measurements should allow a better evaluation of the factors which influence the resolution in exclusion chromatography. In addition, the diffusion of macromolecules in gels may provide models for the diffusion of these molecules in the cytoplasm of living cells and in connective biological tissues.     

High-performance molecular sieve chromatography of proteins on agarose columns: the relation between concentration and porosity of the gel

Curves showing the relation between log (molecular weight) and distribution coefficient are presented for proteins subjected to molecular sieve chromatography on crosslinked and non-crosslinked agarose gels of different concentrations. These curves, which facilitate selection of the gel concentration that gives optimal resolution in any particular separation problem, show that the exclusion limit of 5, 9, 12, and 20% agarose gels correspond to protein with molecular weights above 1,000,000, 600,000, 450,000, and 280,000, respectively. Plate numbers have been determined for columns of 20% agarose at different flow rates and bead sizes. Separations of model proteins by high-performance molecular sieve chromatography on agarose beads are shown.     

Transmembrane permeability channels in vesicles reconstituted from single species of porins from Salmonella typhimurium.

Aggregates of the "major" outer membrane proteins, "porins," of Salmonella typhimurium form diffusion channels in reconstituted vesicle membranes. The aggregate consists of three species of porins with apparent molecular weights of 34,000, 35,000, and 36,000 when active aggregates are subjected to sodium dodecyl sulfate-acrylamide gel electrophoresis after heating in the presence of sodium dodecyl sulfate (Nakae, J. Biol. Chem. 251:2176-2178, 1976). Single species of porins were isolated by solubilization of membranes and subsequent gel filtration in the presence of sodium dodecyl sulfate from the mutant strains of Salmonella typhimurium that produced only single species of porin. The single species of porins of either 34,000, 35,000, or 36,000 daltons formed diffusion channels when assayed for sucrose permeability in the vesicle membranes reconstituted from porins, phospholipids, and lipopolysaccharides. The exclusion limits of the pores made of single species of porins were not distinguishable from each other and from the exclusion limits of the pores made of the porin aggregates from the wild-type strain, when the permeability of vesicle membranes to radioactive di-, tri-, and tetrasaccharides and to various sizes of radioactive polyethylene glycol was determined. Porin-deficient mutants produced residual amounts of porin amounting to 1 to 5% that produced by the parent strain. This residual porin made diffusion channels when the isolated porins were incorporated into the vesicle membrane and assayed for permeability of saccharides.     

Biophysical parameters influence actin-based movement, trajectory, and initiation in a cell-free system

Using a biochemically complex cytoplasmic extract to reconstitute actin-based motility of Listeria monocytogenes and polystyrene beads coated with the bacterial protein ActA, we have systematically varied a series of biophysical parameters and examined their effects on initiation of motility, particle speed, speed variability, and path trajectory. Bead size had a profound effect on all aspects of motility, with increasing size causing slower, straighter movement and inhibiting symmetry-breaking. Speed also was reduced by extract dilution, by addition of methylcellulose, and paradoxically by addition of excess skeletal muscle actin, but it was enhanced by addition of nonmuscle (platelet) actin. Large, persistent individual variations in speed were observed for all conditions and their relative magnitude increased with extract dilution, indicating that persistent alterations in particle surface properties may be responsible for intrinsic speed variations. Trajectory curvature was increased for smaller beads and also for particles moving in the presence of methylcellulose or excess skeletal muscle actin. Symmetry breaking and movement initiation occurred by two distinct modes: either stochastic amplification of local variation for small beads in concentrated extracts, or gradual accumulation of strain in the actin gel for large beads in dilute extracts. Neither mode was sufficient to enable spherical particles to break symmetry in the cytoplasm of living cells.     

THE ORIGIN OF PROTEIN AND FATTY YOLK IN RANA PIPIENS : I. Phase Microscopy

Study of living frog oocytes with the phase microscope has shown that the early yolk appears in two forms. One of these, the protein yolk, consists of thin, dense, plate-like bodies which in face view are almost always regular hexagons. The other form, the fatty yolk, occurs as clusters of globules of varying sizes. The plate-like bodies occur both singly and in clusters. As the oocytes mature these plate-like bodies grow in size while retaining their hexagonal outline. Mitochondria have been observed to increase in length and numbers as the oocytes mature; they are rods or filaments at all stages of growth up to an oocyte diameter of 300 microns. The oocyte cytoplasm gradually becomes packed with long mitochondria, plate-like bodies, and clusters of globules.     

Inhibition of nuclear accumulation of karyophilic proteins in living cells by microinjection of the lectin wheat germ agglutinin

The lectin wheat germ agglutinin (WGA), which has been reported to inhibit nuclear protein uptake in vitro by isolated nuclei (Finlay et al. (1987) J. Cell Biol. 104, 189), also blocks, on microinjection into living cells, the migration of proteins into the cell nucleus. Radioactively labeled nuclear proteins were injected into the cytoplasm of Xenopus oocytes and their reentry into the nucleus was analyzed in the presence or absence of WGA by two-dimensional gel electrophoresis. In another set of experiments, fluorescently labeled nucleoplasmin was injected, alone or together with WGA, into the cytoplasm of rat hepatoma cells, and its nucleocytoplasmic distribution was studied by quantitative laser fluorescence microscopy. The results indicate that WGA inhibits the uptake of karyophilic proteins in general, independent of their sizes. Since the nucleocytoplasmic flux of a dextran with Mr 10,000 was not affected it can be excluded that WGA acts by a general blockade or constriction of the functional pore channel. At reduced WGA concentrations, the rate but not the final extent of nuclear protein accumulation was decreased. These findings support the concept that the O-glycosidically bound carbohydrates of certain nuclear pore complex proteins are exposed to the pore interior and that these regions are probably involved in nucleocytoplasmic translocation processes.     

Protein migration into nuclei. I. Frog oocyte nuclei in vivo accumulate microinjected histones, allow entry to small proteins, and exclude large proteins

A technique is presented which enables one to measure the extent to which a protein enters and accumulates in the nucleus of the frog oocyte. In this method, the protein, labeled with 125-I, is microinjected into the oocyte. After incubation, the oocyte is manually enucleated and the radioactivity in the nucleus and cytoplasm is determined. Using this technique, proteins lighter than 20,000 daltons were found to enter the nucleus and completely equilibrate between the nucleus and cytoplasm within 24 h. The entry of proteins heavier than 69,000 daltons was severely hindered. Histones and histone fractions entered as quickly as other small proteins, but, in contrast to these proteins, they accumulated in the nucleus to different extents, depending on the total amount of histone injected into the oocyte and the identity of the histone. Evidence is presented that histone fractions compete with each other for accumulation in the nucleus.     

Immobilization of proteins on organic polymer beads

A new method is described for the immobilization of biologically active proteins onto several types of organic polymer beads. First, the soluble protein is modified by reaction with an excess of a hydrophobic imidoester, for example methyl 4-phenyl-butyrimidate, at ca. pH 9 and 0 degrees . Excess imidoester and side products resulting from imidoester hydrolysis are separated from the hydrophobic protein derivative by exclusion chromatography or dialysis. A suspension of polymer beads (e.g. Amberlite XAD-7) is then added to a solution of the modified protein at room temperature or below and stirred gently for 1-2 h. The polymer beads are allowed to settle, separated from the solution by decantation or filtration, washed, and resuspended in an appropriate buffer. Quantitative adsorption of protein to the polymer beads is observed under such conditions. The synthesis of seven hydrophobic imidoesters and their use for the immobilization of trypsin onto several types of porous polymer beads is described. The immobilizations of trypsin, yeast alcohol dehydrogenase, and E. coli asparaginase by this procedure with high recoveries of catalytic activity, suggests that it will be applicable to a large number of biologically active proteins.     

Differentiation and distribution of annulate lamellae in growing oocytes in the newt, Cynops pyrrhogaster

Stages of oocyte development in Cynops pyrrogaster are defined, and changes of annulate lamellae in their fine structure, number, sizes and locations during oogenesis are described. The results show that two different types of annulate lamellae occur during oogenesis. One type differentiates in or at the periphery of vesicle-rich cytoplasm at the early stages of vitellogenesis and increases in number and size. The maximum number of about 40 stacks per median section of oocyte is reached at the stage of complete differentiation of the animal and the vegetal hemispheres. In these growing oocytes, all the stacks show elongate appearances and tetragonal arrangements of annuli as common characteristics. A second type of stacks of annulate lamellae is added anew in full-grown oocytes, increasing the number of stacks per median section of the oocyte to about 90. The new stacks occur in close contact with electron-dense bodies in the cytoplasm and have a massive appearance and hexagonal array of annuli. It is suggested that they appear coincidentally with the onset of oocyte maturation. The possible significance of the observed results is discussed.     

Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli.

The very high concentration of macromolecules within cells can potentially have an overwhelming effect on the thermodynamic activity of cellular components because of excluded volume effects. To estimate the magnitudes of such effects, we have made an experimental study of the cytoplasm of Escherichia coli. Parameters from cells and cell extracts are used to calculate approximate activity coefficients for cytoplasmic conditions. These calculations require a representation of the sizes, concentrations and effective specific volumes of the macromolecules in the extracts. Macromolecule size representations are obtained either by applying a two-phase distribution assay to define a related homogeneous solution or by using the molecular mass distribution of macromolecules from gel filtration. Macromolecule concentrations in cytoplasm are obtained from analyses of extracts by applying a correction for the dilution that occurs during extraction. That factor is determined from experiments based upon the known impermeability of the cytoplasmic volume to sucrose in intact E. coli. Macromolecule concentrations in the cytoplasm of E. coli in either exponential or stationary growth phase are estimated to be approximately 0.3 to 0.4 g/ml. Macromolecule specific volumes are inferred from the composition of close-packed precipitates induced by polyethylene glycol. Several well-characterized proteins which bind to DNA (lac repressor, RNA polymerase) are extremely sensitive to changes in salt concentration in studies in vitro, but are insensitive in studies in vivo. Application of the activity coefficients from the present work indicates that at least part of this discrepancy arises from the difference in excluded volumes in these studies. Applications of the activity coefficients to solubility or to association reactions are also discussed, as are changes associated with cell growth phase and osmotic or other effects. The use of solutions of purified macromolecules that emulate the crowding conditions inferred for cytoplasm is discussed.     

Global analysis of gel mobility of proteins and its use in target identification

SDS-PAGE is a basic method that has long been used for separation of proteins according to their molecular sizes. Despite its simplicity, it provides information on characteristics of proteins beyond their molecular masses because gel mobility of proteins often reflects their physicochemical properties and post-translational modifications. Here we report on a global analysis of gel mobility of the proteome, which we term the "mobilitome," covering 93.4% of the fission yeast proteome. To our surprise, more than 40% of proteins did not migrate to their calculated positions. Statistical analyses revealed that the discrepancy was largely dependent on the hydrophobicity of proteins. This experimental data set, with a high coverage rate of real mobility, made it feasible to identify proteins detected on the gel without using any specialized techniques. This approach enabled us to detect previously unknown post-translational modifications of a protein; for example, we revealed that eIF5A is novel substrate of a Sir2-related deacetylase Hst2. Furthermore, we concomitantly identified twelve acetylated and eight methylated proteins using specific anti-acetylated and anti-methylated lysine antibodies, most of which had not been known to be subject to the modifications. Thus, we propose the general usefulness of the mobilitome and electrophoresis-based methodology for the identification and characterization of proteins detected on the gel.