Immunofluorescent subcellular localization of some muscle proteins: A comparison between tissue sections and isolated myofibrils

Summary The localization of parvalbumin in fish white muscle and of the calcium binding protein, of arginine kinase and of glycogen phosphorylase in crayfish tail muscle have been investigated by immunofluorescence using isolated myofibrils and muscle sections as starting materials.It is shown that the four proteins appear to be localized on the thin filaments when myofibrils are used as starting material. This result contrasts with previous observations where it appeared that parvalbumin in fish muscle and arginine kinase in crayfish muscle were distributed uniformly within the cell. This discrepancy is discussed in relation to the high solubility of these proteins.In the light of the present knowledge about striated muscles from these two organisms, it seems that the roles of parvalbumin in fish and of the calcium binding protein in crayfish are probably different.A preliminary report on this work was presented at the meeting of the Union of Swiss Societies for Experimental Biology, Zurich, 1977 (Benzonana et al., 1977a)     

Immunofluorescent localization of pea storage proteins in glycol methacrylate embedded tissue.

Improved immunofluorescent techniques have been developed for the high resolution light microscopic localization of intracellular antigens in plant tissue. Thin sections of pea cotyledon tissue which had been fixed in paraformaldehyde and embedded in glycol methacrylate were reacted with mono-specific antibodies to the storage proteins legumin and vicilin. These antibodies were raised in sheep, purified by affinity chromatography and tested by immunoelectrophoresis and immunodiffusion. Using the indirect technique, rhodamine-labeled antibodies permitted specific fluorescent localization of the legumin and vicilin to small (ca. 1 micrometer) cytoplasmic organelles in near mature tissue. Subsequent histochemical staining verified the proteinaceous nature of these organelles. Parameters affecting staining specificity and background fluorescence are discussed.     

Predicting subcellular localization of proteins in a hybridization space

MOTIVATION: The localization of a protein in a cell is closely correlated with its biological function. With the number of sequences entering into databanks rapidly increasing, the importance of developing a powerful high-throughput tool to determine protein subcellular location has become self-evident. In view of this, the Nearest Neighbour Algorithm was developed for predicting the protein subcellular location using the strategy of hybridizing the information derived from the recent development in gene ontology with that from the functional domain composition as well as the pseudo amino acid composition. RESULTS: As a showcase, the same plant and non-plant protein datasets as investigated by the previous investigators were used for demonstration. The overall success rate of the jackknife test for the plant protein dataset was 86%, and that for the non-plant protein dataset 91.2%. These are the highest success rates achieved so far for the two datasets by following a rigorous cross-validation test procedure, suggesting that such a hybrid approach (particularly by incorporating the knowledge of gene ontology) may become a very useful high-throughput tool in the area of bioinformatics, proteomics, as well as molecular cell biology. AVAILABILITY: The software would be made available on sending a request to the authors.     

PSLpred: prediction of subcellular localization of bacterial proteins

SUMMARY: We developed a web server PSLpred for predicting subcellular localization of gram-negative bacterial proteins with an overall accuracy of 91.2%. PSLpred is a hybrid approach-based method that integrates PSI-BLAST and three SVM modules based on compositions of residues, dipeptides and physico-chemical properties. The prediction accuracies of 90.7, 86.8, 90.3, 95.2 and 90.6% were attained for cytoplasmic, extracellular, inner-membrane, outer-membrane and periplasmic proteins, respectively. Furthermore, PSLpred was able to predict approximately 74% of sequences with an average prediction accuracy of 98% at RI = 5. AVAILABILITY: PSLpred is available at http://www.imtech.res.in/raghava/pslpred/     

Immunofluorescent and histochemical localization of AMP deaminase in skeletal muscle

Fluorescent antibody staining experiments with both isolated myofibrils and muscle fibers grown in culture show that AMP deaminase is bound to the myofibril in the A band. The strongest staining occurs at each end of the A band. The approximate width of the fluorescent stripes and their relation to the A band remains constant as a function of sarcomere length. Removal of enzyme from the myofibrils leads to loss of staining, and readdition of purified enzyme restores the original staining pattern. A histoenzymatic method for the detection of AMP deaminase activity in cultured fibers gives comparable localization. The results are consistent with the previous observation (Ashby, B. and C. Frieden. 1977.J. Biol. Chem. 252:1869--1872) that AMP deaminase forms a tight complex in solution with subfragment-2 (S-2) of myosin or with heavy meromyosin (HMM).     

Changes in subcellular localization of fructose 1,6-bisphosphatase during differentiation of isolated muscle satellite cells

Subcellular localization of FBPase, a regulatory enzyme of glyconeogenesis, was examined inside dividing and differentiating satellite cells from rat muscle. In dividing myoblasts, FBPase was located in cytosol and nuclei. When divisions ceased, FBPase became restricted to the cytosolic compartment and finally was found to associate with the Z-lines, as in adult muscle. Moreover, a 12-fold decrease was observed in the number of FBPase-positive nuclei associated with muscle fibres of adult rat, as compared with young muscle, possibly reflecting the reduction in number of active satellite cells during muscle maturation. The data might suggest that FBPase participates in some nuclear processes during development and regeneration of skeletal muscle.     

Effect of a serine protease on isolated myofibrils.

Morphological changes occurred in myofibrils prepared from the glycerinated psoas muscle of rabbit during incubation with a serine protease crystallized from rat skeletal muscle. Two notable phenomena were observed: (1) loss of the Z band in the early stage of incubation and (2) complete disappearance of the A band after swelling of the myofibrils. The results indicate that the serine protease has an action on myofibrils different from that of Ca2+-dependent neutral protease.     

Metabolism of cartilage proteins in cultured tissue sections.

The asparagine-linked oligosaccharides of the complex acidic-type from [3H]mannose-, [3H]glucosamine- or [3H]galactose-labelled membrane glycoproteins of BHK21 cells and Rous-sarcoma virus were analysed by gel filtration combined with extensive digestion with endo- and exo-glycosidases from bacterial and eukaryotic sources. The neutral products from the digestion with a mixture of exoglycosidases and endo-beta-N-acetylglucosaminidase D from Diplococcus pneumoniae included a series of [3H]mannose- and [3H]glucosamine-labelled neutral oligosaccharides that were all converted by digestion with eukaryotic beta-N-acetylglucosaminidases into free N-acetylglucosamine and a small oligomannosyl core containing two alpha-linked mannose residues and a third mannose residue beta-linked to N-acetylglucosamine. These studies suggested that the complex acidic-type oligosaccharides from cellular and viral membrane glycoproteins contained a common oligomannosyl core region (Man2 alpha leads to Man beta leads to GlcNAc2), with heterogeneity in the number and/or linkage of outer branch N-acetylglucosamine residues resulting in partial resistance to beta-N-acetylglucosaminidase from a bacterial source.     

Immunofluorescent localization of glycogenolytic and glycolytic enzyme proteins and of malate dehydrogenase isozymes in cross-striated skeletal muscle and heart of the rabbit.

Specific antisera against glycogen phosphorylase, phosphofructokinase, aldolase, glyceraldehyde-phosphate dehydrogenase, enolase, lactate dehydrogenase, cytosolic and mitochondrial malate dehydrogenase from rabbit muscle were obtained from sheep. The gamma-globulins were used for indirect immunofluorescent localization of the respective enzymes in rabbit skeletal muscle and heart. In stretched skeletal muscle a cross-striation like distribution was observed for all enzymes studied. In the case of mitochondrial malate dehydrogenase this pattern is due to the staining of I-band mitochondria. In cross-sections, an intense staining of the sarcolemma and of subsarcolemmal mitochondria was observed. Comparative analyses with polarized light revealed that the cytosolic enzymes under study are distributed in the relaxed muscle fibre predominantly within the isotropic zones. The same distribution holds also for heart. In contracting muscle a decrease in cross-striated fluorescence and a faint staining of the interfibrillar spaces suggests a location also within the interfibrillar space.     

Correlation between biochemical properties and adaptive diversity of skeletal muscle myofibrils and myosin of some air-breathing teleosts

Functional properties of myofibrils and relative stability of myosin of five teleosts Channa punctata, Clarias batrachus, M astacembalus armatus, Labeo rohita and Catla catla adapted to different breathing modes were compared. Myofibrillar contractility and m-ATPase of air-breathing organ (ABO) possessing C.punctata and C. batrachus were low and least affected by pH in the range of 7.1-8.5. However, their myosin isoforms were relatively thermostable, more soluble at sub-neutral pH values, between 0.1 to 0.15 M KCl concentrations and less susceptible to a-chymotryptic digestion. In contrast, myofibrils and myosin of water-breather major carps L. rohita and C. catla were more contractile and susceptible to pH and salt concentrations. Thus, correlation between catalytic efficiency and relative stability of myofibrils and myosin of ABO-possessing teleosts was of reverse order and magnitude, as compared to water-breathers. Interestingly, myofibrils and myosin of the behavioral air-breather M. armnatus showed intermediate properties. The specific levels of m-ATPase of all the five teleosts were in conformity with the levels of metabolic marker, the lactate dehydrogenase. The effect of chymotryptic cleavage of 94 and 173 kDa domains on ATPase, individuality of peptide maps of MyHC isomers and perturbation of phenylalanine residues by urea implicated hydrophobic residues in stabilizing myosin structure in these fish. The present study suggests two apparent evolutionary modifications of myofibrils and myosin in ABO-possessing teleosts: (i), 'down-regulation' of ATPase that explains sluggishness of such species and, (ii), more stable molecular structure to support stress of air-breathing modes of life.     

Protein adsorption at polymer-grafted surfaces: comparison between a mixture of saliva proteins and some well-defined model proteins

Grafting a dense layer of soluble polymers onto a surface is a well-established method for controlling protein adsorption. In the present study, polyethylene oxide (PEO) layers of three different grafting densities were prepared, i.e. 10-15 nm2, 5.5 nm2 and 4 nm2 per polymer chain, respectively. The adsorption of different proteins on the PEO grafted surfaces was measured in real time by reflectometry. Furthermore, the change of the zeta-potential of such surfaces resulting from adsorption of the proteins was determined using the streaming potential method. Both the protein adsorption and the zeta-potential were monitored for 1 h after exposure of the protein solution to the surface. The adsorption pattern for a mixture of saliva proteins was compared to those observed for a number of well-defined model-proteins (lysozyme, human serum albumin, beta-lactoglobulin and ovalbumin). The results of the adsorption kinetics and streaming potential measurements indicate that the effect of the PEO layer on protein adsorption primarily depends on the size and the charge of the protein molecules. The saliva proteins are strongly blocked for adsorption, whereas the change in the zeta-potential is larger than for the other proteins (except lysozyme). It is concluded that positively charged protein molecules, having dimensions larger than those of lysozyme, are involved in the initial stage of adsorption from saliva onto a negatively charged surface.     

iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins

Predicting protein subcellular localization is an important and difficult problem, particularly when query proteins may have the multiplex character, i.e., simultaneously exist at, or move between, two or more different subcellular location sites. Most of the existing protein subcellular location predictor can only be used to deal with the single-location or "singleplex" proteins. Actually, multiple-location or "multiplex" proteins should not be ignored because they usually posses some unique biological functions worthy of our special notice. By introducing the "multi-labeled learning" and "accumulation-layer scale", a new predictor, called iLoc-Euk, has been developed that can be used to deal with the systems containing both singleplex and multiplex proteins. As a demonstration, the jackknife cross-validation was performed with iLoc-Euk on a benchmark dataset of eukaryotic proteins classified into the following 22 location sites: (1) acrosome, (2) cell membrane, (3) cell wall, (4) centriole, (5) chloroplast, (6) cyanelle, (7) cytoplasm, (8) cytoskeleton, (9) endoplasmic reticulum, (10) endosome, (11) extracellular, (12) Golgi apparatus, (13) hydrogenosome, (14) lysosome, (15) melanosome, (16) microsome (17) mitochondrion, (18) nucleus, (19) peroxisome, (20) spindle pole body, (21) synapse, and (22) vacuole, where none of proteins included has ≥25% pairwise sequence identity to any other in a same subset. The overall success rate thus obtained by iLoc-Euk was 79%, which is significantly higher than that by any of the existing predictors that also have the capacity to deal with such a complicated and stringent system. As a user-friendly web-server, iLoc-Euk is freely accessible to the public at the web-site http://icpr.jci.edu.cn/bioinfo/iLoc-Euk. It is anticipated that iLoc-Euk may become a useful bioinformatics tool for Molecular Cell Biology, Proteomics, System Biology, and Drug Development Also, its novel approach will further stimulate the development of predicting other protein attributes.