Characterizing proteins in their cellular environment: Examples of recent advances in quantitative fluorescence microscopy

Quantitative characterization of protein interactions, both intramolecular and intermolecular, is crucial in understanding the mechanisms and regulation of their function. In recent years, it has become possible to obtain such information on protein systems in live cells, from bacteria to mammalian cell lines. This review discusses recent advances in measuring protein folding, absolute concentration, oligomerization, diffusion, transport, and organization at super‐resolution.     

Internalized proteins directed into accumulative compartments of mosquito oocytes by the specific ligand, vitellogenin

We have investigated the internalization pathways for a specific protein, vitellogenin, and a non-specific protein, horseradish peroxidase, in the mosquito oocyte in vivo. The internalized proteins were localized by electron microscopical immunocytochemistry or autoradiography; the relationship of their destination compartments with lysosomes was monitored by visualization of acid phosphatase. Proteins internalized by the oocyte follow either a specific accumulative route or a lysosomal degradative route. Via coated vesicles, both proteins enter the same compartment, the endosome, where they dissociate from membrane-binding sites. The route to their final destination depends on the presence of the specific ligand. In its absence, the degradative route is followed, and the endosome with non-specific protein fuses with lysosomes. In the presence of the specific ligand, the accumulative route is followed, and both specific and non-specific proteins are delivered into an accumulative compartment, the transitional yolk body. During the transformation of the transitional yolk body into the final storage compartment, a mature yolk body, vitellogenin undergoes crystallization, whereas the non-specific protein is concentrated in small vesicular extensions of the compartmental membrane. These vesicles are separated from the yolk bodies and apparently deliver the non-specific protein into the lysosomal system. We concluded that any protein bound to the membrane would be internalized by the oocyte, but only binding of the specific ligand to its receptor serves as a transmembrane signal stimulating the formation of accumulative compartments.     

An assay to measure the affinity of proteins for microtubules by quantitative fluorescent microscopy

We report a fluorescence-based assay for measuring the affinity of microtubule binding proteins for microtubules. The affinity of any fluorescently tagged protein for taxol-stabilized microtubules can be measured with this assay. We describe the assay and provide a detailed protocol. Using this assay, we found that the affinity of the Dam1 complex for microtubules is decreased by the presence of free unpolymerized tubulin and is sensitive to the salt concentration in the binding buffer. These effects may account for the previous differences in binding affinities reported.     

Proteomics: quantitative and physical mapping of cellular proteins

Genome sequencing provides a wealth of information on predicted gene products (mostly proteins), but the majority of these have no known function. Two-dimensional gel electrophoresis and mass spectrometry have, coupled with searches in protein and EST databases, transformed the protein-identification process. The proteome is the expressed protein complement of a genome and proteomics is functional genomics at the protein level. Proteomics can be divided into expression proteomics, the study of global changes in protein expression, and cell-map proteomics, the systematic study of protein-protein interactions through the isolation of protein complexes.     

Harnessing the ubiquitination machinery to target the degradation of specific cellular proteins

The functional characterization of a specific gene, or its protein product, often relies on assessing the consequences of its elimination, usually accomplished by gene knockout, ribozyme, antisense, or RNA-mediated interference (RNAi) technologies. The selective degradation of cellular proteins is mediated primarily by the ubiquitin-proteasome pathway. Manipulation of the ubiquitin-dependent proteolytic machinery to eliminate specific gene products at the protein level has been previously attempted with some success in vitro; however, the in vivo efficacy of this approach has not yet been achieved. Here we report successful engineering of the substrate receptor of a major ubiquitin-proteolytic machinery to direct the degradation of otherwise stable cellular proteins both in yeast and in mammalian cells.     

A quantitative method for the measurement of cellular guanosine triphosphate pool specific activities

Studies on quantitation of RNA synthesis in eucaryotic cells have frequently used adenosine as the radioactively labeled precursor, largely because of the convenience of the firefly luciferin-luciferase assay in measuring ATP pool specific activity (1,2). This could result in some difficulties if the addition of poly(A) to the 3′ OH end of RNA represents a significant portion of total incorporation, as is the case in sea-urchin embryos (3). In addition, in some cases, the ATP pool may be large enough to prevent the use of adenosine as an effective labeling agent. Hence, a simple and sensitive method for the determination of the specific activity of the other nucleic acid precursor pools would be of value.Although the crystalline luciferase is specific for ATP, extracts of firefly lanterns most commonly used for quantitating ATP (4–9) also exhibit activity with other ribonucleoside triphosphates, adenosine tetraphosphate, ADP, and the deoxyribonucleoside triphosphates. This activity is due to the presence of contaminating enzymes such as nucleoside 5′-diphosphate kinase and adenylate kinase which catalyze the formation of ATP from these nucleotides and trace amounts of ADP, also present in the extracts (10–13). Recently, Manandhar and Van Dyke (14) have reported a procedure for quantitating picomole levels of GTP with a crude extract of firefly lanterns. In the present study, we have adapted their procedure to develop an assay for GTP pool specific activity in Xenopus laevis oocytes microinjected with [8-³H]GTP. Our assay may be extended to the analysis of any nucleoside triphosphate pool, provided that an adequate chromatography system is available for the separation of the extracted nucleotides.     

Cell cycle-dependent association of HSP70 with specific cellular proteins

In asynchronous populations of HeLa cells maintained at control or heat shock temperatures, HSP70 levels and its subcellular distribution exhibit substantial heterogeneity as demonstrated by indirect immunofluorescence with HSP70-specific monoclonal antibodies. Of particular interest is a subpopulation of cells in which the characteristic nuclear accumulation and nucleolar association of HSP70 is not detected after heat shock treatment. This apparent variation in the heat shock response is not observed when synchronized cells are examined. In this study, we demonstrate that three monoclonal antibodies to HSP70, in particular, do not detect nucleolar-localized HSP70 in heat-shocked G2 cells. This is not due to an inability of G2 cells to respond to heat shock as measured by increased HSP70 mRNA and protein synthesis, or due to a lack of accumulation of HSP70 after heat shock in G2. Rather the epitopes recognized by the various antibodies appear to be inaccessible, perhaps due to the association of HSP70 with other proteins. Non-denaturing immunoprecipitations with these HSP70-specific antibodies suggest that HSP70 may interact with other cellular proteins in a cell cycle-dependent manner.     

Binding of proteins to specific target sites in membranes measured by total internal reflection fluorescence microscopy

A new quantitative technique for measuring the binding of proteins to membranes is described. The method is based on a combination of total internal reflection fluorescence microscopy and the preparation of supported planar bilayers. Specific and reversible binding of a fluorescence-labeled monoclonal antibody to lipid haptens that were embedded in supported bilayers has been measured by this technique and compared to binding experiments that were conducted on membrane vesicles in solution. Equilibrium binding constants and kinetic parameters have been determined and used to expand the picture of the antibody-lipid hapten reaction. Estimates demonstrate that this technique is capable of measuring a broad range of binding constants (down to about 10(4) M-1) using only small amounts of ligand and receptor.     

GFP-tagged proteins visualized by freeze-fracture immuno-electron microscopy: a new tool in cellular and molecular medicine

GFP-tagging is widely used as a molecular tool to localize and visualize the trafficking of proteins in cells but interpretation is frequently limited by the low resolution afforded by fluorescence light microscopy. Although complementary thin-section immunogold electron microscopic techniques go some way in aiding interpretation, major limitations, such as relatively poor structural preservation of membrane systems, low labelling efficiency and the two-dimensional nature of the images, remain. Here we demonstrate that the electron microscopic technique freeze-fracture replica immunogold labelling overcomes these disadvantages and can be used to define, at high resolution, the precise location of GFP-tagged proteins in specific membrane systems and organelles of the cell. Moreover, this technique provides information on the location of the protein within the phospholipid bilayer, potentially providing insight into mis-orientation of tagged proteins compared to their untagged counterparts. Complementary application of the freeze-fracture replica immunogold labelling technique alongside conventional fluorescence microscopy is seen as a novel and valuable approach to verification, clarification and extension of the data obtained using fluorescent-tagged proteins. The application of this approach is illustrated by new findings on PAT-family proteins tagged with GFP transfected into fibroblasts from patients with Niemann-Pick type C disease.     

EHD proteins are associated with tubular and vesicular compartments and interact with specific phospholipids

The four Eps15 homology (EH) domain-containing proteins, EHD1-EHD4, have recently been ascribed roles in the regulation of the recycling of distinct receptor molecules and are often found associated with tubular structures. Here, we report the analysis of all four EHD proteins with regard to tissue distribution, intracellular localization and lipid binding properties. Specific antibodies reveal distinct expression profiles for the individual proteins in tissues and at intracellular locations, where they potentially interact with specific phospholipids. Moreover, EHD proteins colocalize with vesicular and tubular structures, implying roles in transport processes and cytoskeletal dynamics. Protein variants carrying mutations in the N-terminal nucleotide-binding P-loop region are no longer associated with phospholipids or membrane compartments, while deletion of the C-terminal EH domain affects targeting to tubular structures. All EHD proteins are able to bind to phospholipids, but localizations differ for each protein.     

About possible specialization of different compartments of a motoneuron axon for synthesis of specific proteins

The spontaneous quantum secretion of neurotransmitter and its regulation through the system of presynaptic acetylcholine receptors have been studied on a neuromuscular preparation of rat m. soleus of intact animals and animals in which the axonal transport was blocked via the application of colchicine to the sciatic nerve. It was shown that, after six days of colchicine application, the spontaneous quantum secretion, the reaction of presynaptic membrane, and the reaction of neurosecretory apparatus to the depolarization of nerve endings via increase of the content of potassium ions in the environment and to the activation of presynaptic receptors by carbachol are not disturbed. Keeping in mind a rather short half-life of proteins that take part in the exocytosis and its regulation, it may be concluded that their functioning does not depend on the state of the axonal transport. These data correspond to the hypothesis put forward earlier that the synthesis of some proteins performing their function in nerve terminals occurs directly at the site of their utilization but not in the perikaryon, as it has been traditionally assumed.     

Use of a hapten specific anti-dansyl antibody for the localization of ribosomal proteins by immuno electron microscopy

The fluorescent reagent dansyl chloride has been used as an immunological marker for the electron microscopic localization of ribosomal proteins on the surface of 50S ribosomal subunits. The proteins BstL1 from Bacillus stearothermophilus and EcoL1 from Escherichia coli were dansylated to various degrees and reconstituted into the L1-deficient E. coli 50S subunits from mutant MV17-10. Using antibodies specific to dansyl chloride, both proteins were mapped at the lateral protuberance near the peptidyl transferase center.     

A sensitive and specific method for quantitative estimation of carbamylation in proteins

A simple, rapid, reproducible, and specific micromethod for the estimation of carbamylation of proteins is described. The method is based on permanganate oxidation of radioactive carbamyl derivatives of protein to form urea and on the specific decomposition of urea by urease.     

Production of specific antibodies to contractile proteins and their use in immunofluorescence microscopy

Summary The preparation of highly purified myosin from surgical specimen of human uterine muscle is described. Antibodies were raised in rabbits against this immunogen. In immunodiffusion, they react with uterine and chicken gizzard muscle myosin, no reaction is observed between uterine myosin and the anti-chicken-gizzard- myosin. In immunofluorescence, antiuterine-myosin stains smooth muscle in the contractile and modulated state and non-muscle cells such as fibroblasts, platelets and endothelium of various species. Thus, these antibodies contrast anti-gizzard-myosin, which has previously been shown to be specific for contractile state muscle cells. We therefore conclude that the uterine myosin preparation consists of two immunogens, the one being associated with cell contractility and the other, termed cytoplasmic myosin, with motility and mitosis. The latter is indistinguishable from the myosin present in non-muscle cells and can be absorbed specifically with actomyosin from blood platelets.Abbreviations ATP Adenosine triphosphate - DNAse I Deoxyribonuclease I - DTE Dithioerythritol - SDS Sodiumdodecylsulfate - PAGE Polyacrylamide electrophoresis     

Methods for monitoring signaling molecules in cellular compartments

Cells, irrespective of whether they are from multicellular or single-celled organisms, must communicate with the external environment through dynamic regulation of their internal metabolism, which are critical for their survival. Fluorescent and bioluminescent proteins, and related genetic engineering technologies, have provided new opportunities to investigate the molecular dynamics of cells and their internal compartments, with high spatio-temporal resolution. In this review article, since there is a sufficient number of previous reviews summarizing the history of their development and the techniques behind them, here we will focus on molecular features or technologies that have the potential to further open novel investigations of cellular and subcellular dynamics.     

Localization of antioxidant enzymes in the cellular compartments of sorghum leaves

The localization of antioxidant enzymes between the mesophyll and bundle sheath cells were determined in sorghum (Sorghum vulgare L.) leaves. The activity of antioxidant enzymes like superoxide dismutase (SOD), catalase (CAT), guaiacol peroxidase (POD), ascorbate peroxidase (APX) and glutathione reductase (GR) were assayed in whole leaf, mesophyll and bundle sheath fractions of sorghum leaves subjected to water-limited conditions. Drought was imposed by withholding water and the plants were maintained at different water potentials ranging from 0.5–2.0 MPa. The purity of the isolates was tested using the marker enzymes like RuBPcase and PEPcase. GR was mostly localized in mesophyll fraction, while SOD, APX and peroxidase were located in bundle sheath cells. Catalase was found to be equally distributed between the two cell types. Under water stress conditions, most of the SOD activity was found in the bundle sheath tissues. Little or no activity of the enzymes CAT, APX or POD was found in the mesophyll extracts when exposed to water stress. GR activity increased when exposed to low water regimes. From this study, it is clear that antioxidants are differentially distributed between the mesophyll and bundle sheath cells in sorghum leaves. Under water stress conditions, the mesophyll cells showed less damage from oxidative stress when compared to the bundle sheath cells. This is critical for determining the sensitivity of sorghum to extreme climatic conditions.