The detection of DNA-binding proteins by protein blotting

Location of DNA-binding proteins and disulfide-linked proteins in vaccinia virus structural elements

Treatment with sodium dodecyl sulfate (SDS) converted the vaccinia virus strain IHD-J into particles of two types: (i) ghosts which possessed a thin-membrane vesicle derived from basement part of the virus membrane with attached lateral bodies and a membranous structure derived from the core wall and (ii) aggregates of a DNA-nucleoprotein eluted from the core. These particles lacked lipids, and all the viral phospholipids were detected in the SDS-soluble fraction. The viral membrane was composed of an SDS-soluble coat layer and the basement membrane, and the basement membrane was maintained by a mechanism other than the lipid bilayer. By comparisons of protein species in morphologically distinct subviral particles prepared by several solubilizing methods, protein compositions of viral structural elements were suggested as follows: 25,000-molecular-weight viral protein-17,000-molecular-weight viral protein ( VP25K - VP17K ), viral basement membrane; VP13 . 8K , major component of the lateral body; VP70K , VP69K , VP66K , and VP64K , minor components of the lateral body; VP61K , outer layer of core wall; VP57K - VP22K , inner layer of core wall; and VP27K - VP13K , nucleoprotein. These structural elements found in the SDS-insoluble particles dissolved in the same SDS solution under reducing conditions, indicating that the disulfide linkages seem to have a principal role in maintaining their morphological integrity. VP57K , VP27K , VP13 . 8K , and VP13K were revealed to possess affinity for DNA. Denatured calf thymus DNA and viral DNA in double- or single-stranded form associated equally well with these proteins, but RNA did not bind. Therefore, it was strongly suggested that disulfide-linked VP27K - VP13K represented the nucleoproteins of vaccinia virus. A structural model of vaccinia virus is proposed and discussed.

Identification and genetic mapping of a herpes simplex virus capsid protein that binds DNA

Herpes simplex virus virion protein 19C (VP19C) is a constituent of both unenveloped (nuclear) and enveloped (cytoplasmic) capsids. In this paper we report that 32P-labeled DNA, either supercoiled or linear double stranded, efficiently bound to VP19C electrically transferred from denaturing polyacrylamide gels containing electrophoretically separated proteins from purified capsids. Analyses of the polypeptides specified by herpes simplex virus type 1 X herpes simplex type 2 recombinants with respect to electrophoretic mobility and binding of 32P-labeled DNA indicate that VP19C maps at the same location as infected cell polypeptide 32 and is derived from it.

Identification of a rhizosphere protein encoded by the symbiotic plasmid of Rhizobium leguminosarum

A protein was identified which was made by wild-type strains of Rhizobium leguminosarum but not by nodulation-deficient derivatives which had deletions of their symbiotic plasmids. The protein, which had a subunit molecular weight of ca. 24,000 ( 24K ), was found to be present in large amounts within bacteria that had been reisolated from the surface of inoculated pea roots but was not detected in bacteroids isolated from nodules. The protein could also be induced during growth of R. leguminosarum on nutrient medium and was purified from the cytoplasmic fraction of broken cells. Antiserum raised against the purified protein was used to screen transposon-induced mutants of R. leguminosarum, and four independent mutants were isolated which lacked the protein. The sites of the Tn5 insertions were found to map between the nitrogenase and nodulation genes on symbiotic plasmid pRL1JI , ca. 5 kilobases from the nitrogenase genes and 13 kilobases from the nodulation genes. Genetic determinants for the 24K protein were found to be closely linked to plasmid-borne nodulation genes for all strains of R. leguminosarum tested. However, the mutants which lacked the 24K protein still formed normal nitrogen-fixing nodules on peas, and the function of the protein is unknown.

Common non-hormone binding component in non-transformed chick oviduct receptors of four steroid hormones

Steroid hormones produce a response in target cells by binding to hormone-specific soluble receptors, which undergo a transformational change, leading to their interaction with chromatin and to modified gene expression. In a previous paper, we described a monoclonal antibody, BF4, that specifically recognizes and binds the non-transformed '8S' form of chicken oviduct progesterone receptor (8S-PR). We now show that BF4 does not form an immune complex with the 4S transformed form of 3H-progestin-labelled progesterone receptor, but does interact with the 8S non-transformed forms of the oestrogen, androgen and glucocorticosteroid receptors. Our results suggest that the antigenic determinant recognized by BF4 is present on a non-hormone binding unit, which we identify as a polypeptide of molecular weight (MW) 90,000 in the case of the progesterone receptor, and that this unit is common to other 8S non-transformed chicken steroid receptors.

A simple general method of exactly comparing different binding activities and antigenic properties of antibodies by obtaining duplicate copies from a single isoelectric focusing gel

We report a simple general method of exactly comparing different binding activities and/or antigenic properties of antibodies in ascites fluid after fractionation on a single isoelectric focusing gel. Two copies of the gel are made on nitrocellulose: 1 copy is overlaid with the radioiodinated form of one overlay protein and the other copy is overlaid with the radioiodinated form of another. By superimposing X-ray films obtained after radioautography, any 2 binding activities or antigenic properties of antibodies can be compared exactly and in detail. The procedure is simple, highly sensitive, and independent of the molecular weight of the overlay protein. This is accomplished without requiring isolation of the antibodies, denaturing agents, precipitation, chemical fixation or other modification reactions.

Characterization of the precursor form of the exocellular levansucrase from Bacillus subtilis

Expression of the cloned levansucrase gene (sacB) was demonstrated in E. coli minicells by assay of the enzyme in crude extracts, SDS-polyacrylamide gel electrophoresis and immunoblotting. The existence of a precursor form of the enzyme of MW 53000 was also demonstrated and confirmed by the DNA sequence corresponding to the NH2 terminal region of the protein.

It is Rous sarcoma virus protein P12 and not P19 that binds tightly to Rous sarcoma virus RNA

The interactions between Rous Sarcoma virus (RSV) RNA and the viral proteins in the virus have been analysed by Sen & Todaro (1977) using ultraviolet light irradiation; they showed that the major protein ultraviolet light cross-linked to the viral RNA was P19 as identified by polyacrylamide gel electrophoresis. We report here that it is not viral protein P19 but P12 that binds tightly to RSV RNA upon ultraviolet light irradiation of the virus. Therefore, the binding sites of the viral protein along RSV RNA that we have characterized previously should be correctly attributed now to P12 and not P19.

Comparison of the tryptic digestion pattern of subfragments 1 from V1 and V3 rat cardiac isomyosins

The limited tryptic digestion patterns of the chymotryptic subfragment 1 (S1) of the two rat ventricular isomyosins V1 and V3, were compared under several conditions. Pure S1V1 was obtained from 3-week-old rats and pure S1V3 from adult rats 6 weeks after hypophysectomy. To localize the sites of trypsin susceptibility and to determine the distribution of the peptides along the S1 molecule, we used, as a probe, antibodies raised against a pig cardiac 29-kDa peptide. We demonstrate that this peptide contains the N-acetyl group located on the N-terminal part of the cardiac myosin molecule. In S1V1 we observed two major sites of proteolysis, independently of the digestion conditions: they are located at 27kDa and 80kDa from the N terminus as in skeletal muscle S1.S1V3 appears much more sensitive to the proteolysis conditions: at least two additional sites of cleavage are present in the 50-kDa peptide when digested at pH 8.0. Decrease in the pH from 8.0 to 7.0 or the presence of Mg-ATP have no effect on the digestion of S1V1 while these ambient factors protect the 50-kDa peptide of S1V3 from breakdown. We conclude that the 50-kDa peptide is a variable portion of the myosin molecule, the conformation of which is sensitive to ambient factors such as the pH or the presence of nucleotides.

Purification by affinity chromatography and immunological characterization of a 110kDa component of the chick oviduct progesterone receptor

A 110kDa component of the chick oviduct progesterone receptor (PR) has been purified to homogeneity according to electrophoretic criteria and specific activity (assuming one progestagen-binding site/110kDa). The procedure involved affinity chromatography of 0.3 M-KCl-prepared cytosol, followed by DEAE-Sephacel chromatography (elution at 0.2 M-KCl). The final yield was about 12% in terms of binding activity. Properties of the 110kDa component indicate that it is identical with the 'B' subunit described previously [Stokes radius approximately 6.1 nm; sedimentation coefficient, (S20, w) approximately 4S; frictional ratio approximately 1.77]. It reacted with the IgG-G3 polyclonal antibody, but not with BF4 monoclonal antibody raised against the 8S molybdate-stabilized chick oviduct PR and reacting with its 90kDa component. Another progesterone-binding component, corresponding to the 'A' subunit, also previously described, was eluted from the DEAE-Sephacel column at approximately 0.08 M-KCl, and contained a peptide of molecular mass approx. 75-80kDa, which had S20, w approximately 4S in a sucrose gradient. This component was also recognized by IgG-G3, but not by BF4; it was very unstable in terms of hormone-binding activity.

Identification of immunologically cross-reactive proteins of Sindbis virus: evidence for unique conformation of E1 glycoprotein from infected cells

Hyperimmune antisera to purified Sindbis (SIN) or Semliki Forest (SF) virus were used to identify alphavirus-specific and cross-reactive proteins in virions and infected cells. The hyperimmune sera participated in homologous and cross-cytolysis of alphavirus-infected cells, and the use of monospecific antisera to SIN structural proteins suggested that E1 and E2 could serve as target proteins in cytolysis. Proteins from purified virions or infected cells were extracted with Nonidet P-40, denatured by procedures for sodium dodecyl sulfate-polyacrylamide gel electrophoresis, transferred to nitrocellulose solid supports, and reacted with hyperimmune sera and 125I-labeled protein A (immunoblotting on denatured proteins). Alternatively, native proteins extracted by mild Nonidet P-40 treatment were precipitated with hyperimmune sera before denaturation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. After immunoblotting, homologous antiserum reacted with the virus structural proteins E1, E2, capsid extracted from purified virions, and the counterparts of these proteins extracted from infected cells. In addition, PE2 and a 92,000-molecular-weight protein from infected cells reacted with homologous antiserum. These proteins were also immunoprecipitated with homologous antiserum. After immunoblotting, the Sindbis capsid protein was shown to be cross-reactive whether derived from purified virions or from infected cells; no cross-reactivity was observed with PE2 or E2 from either source, and the E1 glycoprotein was shown to be cross-reactive only when obtained from virions. However, the E1 glycoprotein could be cross-immunoprecipitated from infected cells (as well as from disrupted virions), and, in addition, capsid and a 92,000-molecular-weight protein were cross-immunoprecipitated from infected cells. These results suggest that a native conformation of the cell-associated E1 glycoproteins may be required for immunological cross-reactivity (immune precipitation), whereas virion but not cell-associated E1 retains immunological cross-reactivity after denaturation (immunoblot technique). The findings extend our previously published evidence which suggested that alphavirus maturation is accompanied by a change in immunological cross-reactivity with respect to E1.

Synthesis and assembly of the cytoskeleton of Naegleria gruberi flagellates

When Naegleria gruberi flagellates were extracted with nonionic detergent and stained by the indirect immunofluorescence method with AA-4.3 (a monoclonal antibody against Naegleria beta-tubulin), flagella and a network of cytoskeletal microtubules (CSMT) were seen. When Naegleria amebae were examined in the same way, no cytoplasmic tubulin-containing structures were seen. Formation of the flagellate cytoskeleton was followed during the differentiation of amebae into flagellates by staining cells with AA-4.3. The first tubulin containing structures were a few cytoplasmic microtubules that formed at the time amebae rounded up into spherical cells. The formation of these microtubules was followed by the appearance of basal bodies and flagella and then by the formation of the CSMT. The CSMT formed before the cells assumed the flagellate shape. In flagellate shaped cells the CSMT radiate from the base of the flagella and follow a curving path the full length of the cell. Protein synthetic requirements for the formation of CSMT were examined by transferring cells to cycloheximide at various times after initiation. One-half the population completed the protein synthesis essential for formation of CSMT 61 min after initiation of the differentiation. This is 10 min after the time when protein synthesis for formation of flagella is completed and 10-15 min before the time when the protein synthesis necessary for formation of the flagellate shape is completed.

Conservation of interphase chromatin nonhistone antigens as components of metaphase chromosomes

The degree of conservation of HeLa interphase chromatin nonhistone antigens among the nonhistones of isolated metaphase chromosomes was determined with immunological procedures. Proteins were separated on SDS-polyacrylamide gels and electrophoretically transferred to diazophenylthioether (DPT)-paper, which was then overlaid with antiserum to chromatin from interphase nuclei. The bound antibodies were detected with 125I-labeled protein A. Alternatively, polyacrylamide gels were directly overlaid with antiserum and with 125I-protein A. Densitometry of autoradiograms and stained gels revealed the degree of conservation of nonhistone antigenic determinants from interphase to metaphase to be over 90% for chromatin.

Comparison of ribosomal proteins of chloroplast from spinach and of E. coli

A comparison of ribosomal proteins from Escherichia coli and from chloroplasts of Spinach was made using two separate methods: electrophoretic migration and immunochemical cross-reaction between blotted E. coli ribosomal proteins and chloroplast ribosomal subunits antisera. It is shown that L2 from E. coli (E-L2) and L4 from chloroplasts (CS-L4) comigrated and that E-L2 immunologically cross-reacted with the isolated CS-L4 antibody. Co-migration was observed for three additional couples of 50S ribosomal proteins. It is also shown that at least one 30S E. coli ribosomal protein immuno-cross reacted with a 30S chloroplast antiserum and that three couples of 30S ribosomal proteins comigrated.

Two nuclear DNA binding proteins of Dictyostelium discoideum with a high affinity for poly(dA)-poly(dT)

Intergenic regions of the Dictyostelium genome contain an extremely high proportion of AT base pairs. Those intergenic regions which have been subjected to nucleotide sequence analysis are predominantly composed of alternating runs of poly(dA) and poly(dT) and there is evidence to suggest that nucleosomes do not form on such sequences. We have identified two nuclear proteins, of molecular weight 70,000 and 74,000 daltons, which bind only to intergenic regions of a cloned Dictyostelium gene. Binding is specifically inhibited in the presence of synthetic poly(dA) - poly (dT) as competitor. These proteins may play some role in the chromosomal organization of intergenic regions in Dictyostelium discoideum.

Binding of a Glycera convoluta neurotoxin to cholinergic nerve terminal plasma membranes

The crude extract of venom glands of the polychaete annelid Glycera convoluta triggers a large Ca2+-dependent acetylcholine release from both frog motor nerve terminals and Torpedo electric organ synaptosomes. This extract was partially purified by Concanavalin A affinity chromatography. The biological activity was correlated in both preparations to a 300,000-dalton band, as shown by gel electrophoresis. This confirmed previous determinations obtained with chromatographic methods. This glycoprotein binds to presynaptic but not postsynaptic plasma membranes isolated from Torpedo electric organ. Pretreatment of intact synaptosomes by pronase abolished both the binding and the venom-induced acetylcholine release without impairing the high K+-induced acetylcholine release. Pretreatment of nerve terminal membranes by Concanavalin A similarly prevented the binding and the biological response. Binding to Torpedo membranes was still observed in the presence of EGTA. An antiserum directed to venom glycoproteins inhibited the neurotoxin so we could directly follow its binding to the presynaptic membrane. Glycera convoluta neurotoxin has to bind to a ectocellularly oriented protein of the presynaptic terminal to induce transmitter release.

Changes in pattern and accessibility for 125I-labelling of cell-surface proteins after mesenchymal differentiation of embryonal carcinoma cells

Cell-surface proteins of the embryonal carcinoma line C17-S1 1003 (1003) and of some of its mesenchymal derivatives were studied. The surface proteins were labelled with 125I using the lactoperoxidase-glucose-glucose oxidase system either on the cells attached to the culture dishes or after their dissociation. Iodinated proteins were analyzed by two-dimensional gel electrophoresis. The patterns obtained with embryonal carcinoma cells 1003 and with two mesenchymal cell types derived from them, namely embryonic mesenchymal cells (line 10035) and fibroblastic cells (line 10031), were different one from the other, especially when considering the group of proteins labelled on the attached cells. The pattern of cell-surface proteins of the myoblastic line 1168, also derived from C17-S1, was found to be similar to that of 10031 fibroblastic cells. This result is discussed in the light of the phenotypic transition toward myogenesis, which can be obtained with 10031 fibroblastic cells but not with 10035 embryonic mesenchymal cells. A direct method of detection of lectin-binding proteins permitted us to identify the major concanavalin A-binding proteins. Two of them are common to all cell lines studied. They were labeled with 125I on the attached undifferentiated 1003 cells, while in all differentiated derivatives they became available for labelling after the cell detachment only.

Uridine-33 in yeast tRNA not essential for amber suppression

The nucleotide at position 33 on the 5' side of the anticodon of almost all tRNAs is a uridine. Crystallographic studies of different tRNAs reveal that although the precise orientation of uridine-33 is not always the same, it connects the anticodon stacked along the 3' side of the loop with the pyrimidine-32 stacked on the 5' side of the loop. The remarkably conserved nature of uridine-33 and its unique position in the anticodon loop structure has led to suggestions that this nucleotide has an essential role in the translational mechanism. We have developed a biochemical procedure to replace nucleotides 33-35 in yeast tRNATyr with any desired sequence and used it to construct amber suppressor tRNAs having different nucleotides at position 33. As all of these synthetic amber suppressor tRNAs functioned well in eukaryotic in vitro suppression assays, we conclude that uridine-33 does not have an obligatory role in the translation mechanism.

Nucleotide sequence of the trpD and trpC genes of Salmonella typhimurium

We have completed the nucleotide sequence determination of trpD and trpC, the second and third genes of the trp operon of Salmonella typhimurium. These genes encode two bifunctional proteins thought to have arisen by gene fusions: the trpD polypeptide contains the glutamine amido transferase and the phosphoribosyl anthranilate transferase activities, and the trpC protein possesses the N-(5'-phosphoribosyl)-anthranilic acid isomerase and the indole-3-glycerol phosphate synthetase activities. The trpD gene consists of 1593 nucleotides encoding 531 amino acids, and possesses an internal promoter (p2) located within a region from about 1400 to 1441 of the nucleotide sequence. The trpC gene contains 1356 nucleotides encoding 452 amino acids. In this paper we compare the trpD and trpC genes of S. typhimurium to those of Escherichia coli with respect to codon usage, nucleotide and amino acid conservation, p2 promoter characteristics and intercistronic regions. The sequence of the two genes we present here completes the sequence determination of the trp operon of S. typhimurium and should prove useful in comparisons with the E. coli trp operon and in future studies of operon structure in S. typhimurium.

Use of human antibodies to identify antigens in cultured human tumor cells: detection of discrete antigen molecules using electroblotting and enzyme-linked antibody probes

To demonstrate antigens in cultured human tumor cells recognized by antibodies in human sera, extracts of cultured malignant melanoma cells were separated by SDS-PAGE, and electrophoretically transferred to nitrocellulose paper (NCP). The resulting electroblots were incubated with human serum, and bound immunoglobulin (Ig) was visualized with rabbit antibodies specific for human IgG, IgA or IgM, followed by peroxidase-conjugated goat anti-rabbit IgG. Antigen-antibody reactions in the nitrocellulose paper were also detected using 125I-labeled anti-rabbit IgG. As little as 125 pg of bound antibody per band were detectable. The numbers of proteins recognized by antibodies in human sera depended both on the quantity of protein transferred and the concentration of Ig applied to the NCP. Whole serum could not be used at dilutions less than or equal to 1:20 without an unacceptable increase in background staining. Binding of Ig to tumor cell proteins transferred to NCP depended on interactions with the Fab', not the Fc region of the Ig molecule. To determine the efficiency of transfer as a function of both time and molecular weight, tumor cell proteins were intrinsically labeled with 75Se-labeled methionine and transferred for up to 4 h after fractionation in gels containing acrylamide concentrations of 5%, 7.5%, 10% or 12%. Proteins less than 150 kDa were transferred with particularly high efficiency in greater than or equal to 2 h. Different antigens were recognized by the IgA, the IgG and the IgM molecules from the same sera. The methods outlined herein are proving to be useful in monitoring the purification of specific antigens from whole tumor cell extracts.

Nonhistone protein with high affinity for histone H1 and HMG 14 protein

Specific interaction of a nonhistone protein from mouse spleen chromatin with histones HI, H2A and HMG 14 protein is shown. Some implications of these findings are briefly discussed.

Differential binding of nonhistone chromosomal proteins to the putative mouse origin of replication

Ehrlich ascites tumour (EAT) cells were treated with trioxsalen and ultraviolet light to crosslink DNA in vivo. After the treatment initiation of DNA replication can still occur but elongation is blocked by the crosslinks and this leads to the formation of short DNA fragments containing the origin of replication that can be isolated in double-stranded form after S1 nuclease cutting of the crosslinked DNA (Russev, G. and Vassilev, L. (1982) J. Mol. Biol. 161, 77-87). To assess the affinity of these DNA fragments toward different chromosomal proteins, chromatin was fractionated by SDS-polyacrylamide gel electrophoresis, proteins were transferred to nitrocellulose filters and allowed to interact with in vivo labelled [32P]DNA. The autoradiography of the filters showed that the DNA fraction synthesized between crosslinks and containing the putative mouse origin of replication bound preferentially to several nonhistone proteins, the most strongly binding ones having molecular weights of 64, 68, 72 and 150 kDa.

Efficient transfer of proteins from acetic acid-urea and isoelectric-focusing gels to nitrocellulose membrane filters with retention of protein antigenicity

A method which facilitates the rapid and quantitative electrophoretic transfer of proteins from gels not containing sodium dodecyl sulfate (SDS) to nitrocellulose membranes is described. The equilibration of non-SDS-polyacrylamide gel electrophoretic gels in a buffer containing SDS confers a net negative charge to the proteins present, presumably as a result of the formation of SDS-protein complexes. Proteins from gels equilibrated in the SDS buffer and then electroblotted in a Tris-glycine buffer at pH 8.3 are transferred with much greater efficiency than are proteins from untreated gels. The method has been shown to significantly enhance the electrophoretic transfer of polyoma viral proteins resolved in either acetic acid-urea or isoelectric-focusing gels to nitrocellulose membranes, and it is suggested that the method should have universal applicability to all gel electrophoresis systems currently employed. The proteins from isoelectric-focusing gels treated with SDS and transferred to nitrocellulose membranes were found to retain antigenicity to antisera prepared against either denatured or native viral proteins.

Ionic interactions between proteins in nonequilibrium pH gradient electrophoresis: histones affect the migration of high mobility group nonhistone chromatin proteins

In two-dimensional gel electrophoresis of the high mobility group (HMG) proteins, it has proved necessary to use nonequilibrium pH gradient electrophoresis (NEPHGE) in the first dimension rather than isoelectric focusing, because of the basic character of most of the HMG proteins [D. Tyrell, P. J. Isackson, and G. R. Reeck (1982) Anal. Biochem. 119, 433-439]. In this paper it is reported that in samples that contain histones, the mobilities of HMG proteins (particularly HMG-1, HMG-2, and HMG-E) are severely distorted in NEPHGE. This presumably results from formation of complexes between histones and HMG proteins through ionic interactions. Analysis of HMG proteins by NEPHGE/sodium dodecyl sulfate-gel electrophoresis is thus precluded in samples containing histones. Our results raise the possibility of similar artifacts occurring in NEPHGE (or isoelectric focusing) analysis of other proteins with regions of high charge density.

Serum spreading factor (vitronectin) is present at the cell surface and in tissues

Monoclonal antibodies were prepared against a cell attachment-promoting protein, serum spreading factor, which had been partially purified from human serum by chromatography on glass bead columns. The antibodies selected were those that reacted with polypeptides that had cell attachment-promoting activity after sodium dodecyl sulfate/polyacrylamide gel electrophoresis. Immunochromatography of human plasma on columns containing the monoclonal antibodies followed by affinity chromatography on heparin-Sepharose yielded material that in sodium dodecyl sulfate/polyacrylamide gel electrophoretic analysis gave polypeptides of molecular mass 65 and 75 kilodaltons. Both polypeptides bound each of three monoclonal antibodies and had cell attachment-promoting activity after transfer to nitrocellulose filters. Immunofluorescent staining of tissues with the monoclonal antibodies revealed a fibrillar pattern that was mostly associated with loose connective tissue and overlapped with fibronectin fibrils. Fetal membrane tissue, which showed strong staining with the antibodies in immunofluorescence, also gave 65- and 75-kilodalton polypeptides with cell attachment-promoting activity after chromatography on columns containing the monoclonal antibodies. One source of the tissue protein may be fibroblastic cells, because cultured human fibroblasts also stained with the monoclonal antibodies. The staining was fibrillar and appeared to be associated with the cell surface extracellular matrix. We propose the name "vitronectin" for the various forms of this protein, on the basis of its binding to glass and its adhesive properties.

DNA-binding proteins of Haemophilus influenzae: purification and characterization of a major intracellular binding protein

A heat- and acid-stable protein which bound both native and denatured DNA but not RNA was extensively purified from extracts of Haemophilus influenzae Rd strain com-58-A. The active species had an apparent subunit molecular weight of 15,000. The interaction of the protein with denatured DNA appeared to be cooperative, as judged by the sigmoid shapes of binding curves. This cooperativity increased with increasing ionic strength and was more pronounced with sodium ions than with potassium ions. Gel filtration suggested that the native protein formed aggregates in solution. The presence of the binding protein protected single-stranded DNA from the action of S1 endonuclease; approximately 30 nucleotide residues were protected per subunit equivalent of protein. The number of subunit equivalents per cell of this protein has been estimated at 10,000. The protein, which we designate DNA-binding protein II, is most probably a major histone-line protein of H. influenzae.

Interaction of nucleic acids with the DNA-dependent RNA polymerases of Drosophila

The interaction between the three Drosophila DNA-dependent RNA polymerases (EC 2.7.7.6) and the DNA template or the RNA product was investigated by photochemical cross-linking and binding studies, using RNA polymerase subunits immobilized on nitro-cellulose filters. It can be shown that the two largest subunits are responsible for the binding of the enzymes to both template and newly-synthesized RNA.

Nonpackaging and packaging proteins of hnRNA in Drosophila melanogaster

Monoclonal antibodies have previously been raised against chromosomal proteins of Drosophila. Using a biochemical fractionation method for the isolation of large hnRNA-containing structures (hnRNP) of Drosophila tissue culture cells, we show that seven of these antibodies recognize different antigens, and that these antigens are associated with RNA. Analysis of the sedimentation behavior of antigen-containing structures in sucrose gradients reveals that the antigens are differentially distributed with respect both to one another and to pulse-labeled RNA. We demonstrate that the antigens are minor components of hnRNP and are different from the major Drosophila hnRNP packaging proteins, which we have also identified. The antigens are probably involved in the processing of hnRNA in the nucleus.

Temporal order of chromatin structural changes associated with activation of the major chicken vitellogenin gene

The major chicken vitellogenin (VTG II) gene is marked at the chromatin level in hormone-responsive cells by a set of nuclease-hypersensitive sites that exist prior to hormone-mediated expression. When the gene is transcriptionally activated in the liver by treatment with 17 beta-estradiol, three additional hypersensitive sites are induced, which map near the 5' end of the gene. Two of these sites are stable and, moreover, appear to be propagated to daughter cells after hormone is withdrawn. In contrast, the third site (located 0.7 kb upstream from the gene) is observed only during periods of hormone treatment, perhaps due to a transient interaction with hormone receptor complex at this site. Whereas none of these nuclease-hypersensitive sites is observed in erythrocytes, brain, or fibroblasts, a subset is present in differentiated oviduct cells that have estrogen receptors, but do not express VTG II.

Sodium dodecyl sulfate-mediated transfer of electrophoretically separated DNA-binding proteins

A modified procedure for the transfer of electrophoretically-separated proteins from sodium dodecyl sulfate (SDS)-polyacrylamide gels onto nitrocellulose filters has been developed. During the diffusion mediated transfer, the SDS-protein complexes were maintained and SDS was added to the buffer. This increases the number of polypeptide species bound to the filter thereby giving an accurate replica of the original gel pattern. The immobilization in the gel of certain polypeptides characterized as DNA-binding proteins, which is observed when SDS is eliminated prior to blotting is avoided. The molecules blotted in the presence of SDS remain immunoreactive and able to bind DNA.

Why are two different types of pyridine nucleotide transhydrogenase found in living organisms?

Two types of pyridine nucleotide transhydrogenases have been reported in living organisms. The energy-linked transhydrogenase is found in mitochondria and in certain heterotrophic and photosynthesizing bacteria, while the non-energy-linked transhydrogenase is found in certain heterotrophic bacteria. The presence of a structurally similar non-energy-linked transhydrogenase in Azotobacter vinelandii, Pseudomonas aeruginosa and Pseudomonas fluorescens is readily shown in extracts from these bacteria with Western (protein) blotting. This non-energy-linked enzyme is lacking in Escherichia coli, while the presence of a structurally similar energy-linked enzyme in E. coli and in beef heart mitochondria is indicated with the Western blotting technique. Spinach (Spinacia oleracea) lacks the non-energy-linked transhydrogenase occurring in bacteria. The chloroplast enzyme ferredoxin:NADP+ oxidoreductase, which exhibits non-energy-linked transhydrogenase activity, is immunologically distinct from the bacterial transhydrogenases. In order to provide a rationale for the distribution of the two types of pyridine nucleotide transhydrogenases, the steady-state degrees of reduction of the NADP(H) and NAD(H) pools in A. vinelandii (R'NADP(H) and R'NAD(H)) have been measured for cells metabolizing sucrose at a variable oxygen flux (phi O2). It is found that the degree of reduction of the NADP(H) pool is always higher than that of the NAD(H) pool (R'NADP(H) greater than R'NAD(H)) except when phi O2 goes to zero (R'NADP(H) approximately equal to R'NAD(H)). Comparison of these results with literature values indicates that the inequality R'NADP(H) greater than R'NAD(H) is always found in a membrane-enclosed compartment, irrespective of the type of transhydrogenase present. This allows an understanding of the function of the two types of pyridine nucleotide transhydrogenases in vivo. The physiological role of non-energy-linked transhydrogenase is to catalyze the reaction NADPH + NAD+ leads to NADP+ + NADH, that of energy-linked transhydrogenase to catalyze the reaction NADH + NADP+ leads to NADPH + NAD+. Since at equilibrium R'NADP(H) approximately equal to R'NAD(H) the inequality R'NADP(H) greater than R'NAD(H) under steady-state conditions explains the energy requirement in the latter reaction. The dependence of the non-energy-linked transhydrogenase activity of ferredoxin:NADP+ oxidoreductase on R'NADP(H) is compared with that of A, vinelandii transhydrogenase. The results indicate that this activity is unlikely to be of physiological importance in plant chloroplasts.

Isolation of a 167 basepair chromatosome containing a partially digested histone H5

A test has been made of the proposal that protection of the 167 basepair DNA length in the 'chromatosome' is due only to the central globular domain of the lysine-rich histones. Chicken erythrocyte chromatin was treated with trypsin to leave only the limit peptide from histones H1 and H5. Nucleosome monomers were then isolated on sucrose gradients following micrococcal nuclease digestion and were found to contain the 167 basepair DNA band as in intact chromatin. The presence of the limit peptide from H5 on the monomers was confirmed using an antibody to H5. It is concluded that the trypsin-susceptible domains of the lysine-rich histones are not involved in the protection of the 2-turn 167 basepair length of DNA in the nucleosome.

Analysis of receptor-ligand interactions using nitrocellulose gel transfer: application to Torpedo acetylcholine receptor and alpha-bungarotoxin

A nitrocellulose-gel transfer technique has been adapted to study the interaction of a polypeptide ligand with individual receptor subunits. The acetylcholine receptor isolated from Torpedo californica has been separated into its subunits by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and transferred in a renaturing environment to nitrocellulose sheets. The sheets were incubated with 125I-alpha-bungarotoxin and autoradiographed. A single receptor polypeptide, the alpha subunit (40K) bound the labeled toxin. This binding was demonstrated to be both saturable and specific, although the affinity of 125I-alpha-bungarotoxin (KD, 165 nM) and the potency of d-tubocurarine to displace this binding (IC50, 1 mM) were both reduced by several orders of magnitude when compared to the native receptor.

Identification of specific proteins and glycoproteins associated with membrane fractions isolated from Zea mays L. coleoptiles

The aim of this work was to identify proteins specific for plant cell membranes which could then be used as unique markers. A crude membrane fraction was isolated from corn coleoptiles and separated on non-linear sucrose density gradients. Separation of endoplasmic reticulum (NADH-cytochrome c reductase), mitochondria (cytochrome c oxidase), golgi (inosine diphosphatase), and plasma membranes (N-1-naphthylphthalamic acid-binding) was achieved. The membrane proteins from the gradient fractions were separated using sodium dodecyl sulphate-poly-acrylamide gel electrophoresis and the gels stained with coomassie blue or with concanavalin A/peroxidase to detect glycoproteins. Proteins specific for the various membranes were identified. Five proteins including two glycoproteins were plasma membrane markers. Protoplasts were isolated and iodinated using lactoperoxidase/glucose oxidase covalently attached to beads. Eleven iodinated proteins were found and three of these corresponded to proteins specifically associated with plasma membranes in the density gradients. Two methods for detecting Ca(2+)-binding proteins following sodium dodecylsulphate polyacrylamide gel electrophoresis were employed. The majority of such proteins were found in the endoplasmatic reticulum and one was specific for plasma membranes. In vitro and in vivo phosphorylation of membrane proteins was examined and the majority of proteins phosphorylated were glycoproteins. Two of the phosphorylated proteins (Mr=110,000 and 20,000) were also iodinated on protoplasts and may be part of the plasma membrane ATPases.

Chloroplast RNA polymerase from spinach: purification and DNA-binding proteins

Spinach DNA dependent RNA polymerase was purified from isolated chloroplasts by two different procedures. Analysis of the protein composition of the two preparations by SDS-polyacrylamide gel electrophoresis always shows six abundant polypeptides with Mr of 150, 110, 102, 80, 75 and 38 Kd and one less abundant polypeptide of 25 Kd. Some other proteins ranging from 40-70 Kd in Mr are also detected but in a minor and variable amount. The two preparations have an optimum of enzyme activity at 30°C and at 15 mM (NH4)2SO4 when tested with denatured calf thymus DNA.Binding experiments with two different nick translated fragments of spinach chloroplast DNA show that the 80 and 75 Kd polypeptides possess a strong DNA binding capacity.

Monoclonal antibodies to baculovirus structural proteins: determination of specificities by Western blot analysis

Conventional mouse hybridoma technology was utilized to produce a panel of monoclonal antibodies which reacted with baculovirus proteins. Using an enzyme-linked immunosorbent assay (ELISA), the hybridomas which were raised against polyhedrin from Autographa californica nuclear polyhedrosis virus (AcNPV) and Choristoeura fumiferana nuclear polyhedrosis virus (CfNPV) were found to cross-react differentially with polyhedrins and granulins from several species of baculoviruses. Hybridoma antibodies which reacted against the nonoccluded form (NOV) of AcNPV in an ELISA test expressed different specificities for the occluded form of the virus (OV), a mutant strain of AcNPV, and CfNPV. Four hybridoma clones produced antibody which neutralized the infectivity of AcNPV NOV. One hybridoma antibody reacted strongly with the uninfected Spodoptera frugiperda host cell line. Using Western blot analysis, it was shown that hybridoma antibodies against polyhedrin reacted differentially with the complete polypeptide and protease-generated fragments of polyhedrin. The polypeptide specificity of 19 of 28 hybridoma antibodies which reacted with OV and NOV of AcNPV was assigned using Western blot analysis.

Genetic mapping of bra genes affecting branched-chain amino acid transport in Pseudomonas aeruginosa

Pseudomonas aeruginosa PAO mutants defective in the transport systems for branched-chain amino acids were isolated and characterized. Two mutations in strains selected for trifluoroleucine resistance, braA300 and braB307, were mapped in the met-9020-dcu-9108 and the nar-9011-puuC10 region, respectively. The mutation loci in strains selected for azaleucine resistance, braC310 and bra-311 through bra-314, were all located near the fla genes, with an order of region I fla-bra-region II fla. Strains with braA300 showed a marked reduction in the high-affinity branched-chain amino acid transport system (LIV-I) and a considerable decrease in the lower-affinity system (LIV-II). Strains with braB307 were found to be defective in the LIV-II system. Strains selected for azaleucine resistance were all defective only in the LIV-I system and fell into three phenotypically distinct classes. Strains with braC310 produced a binding protein for leucine, isoleucine, valine, alanine, and threonine (LIVAT-BP) altered in binding ability, indicating that the braC gene is the structural one for the LIVAT-BP. Strains with bra-311 or bra-312 showed a complete loss of production of the LIVAT-BP. Strains with bra-313 or bra-314 produced normal levels of functional LIVAT-BP, suggesting that these mutations are located in a gene(s) other than braC.

Ammoniacal silver staining of proteins: mechanism of glutaraldehyde enhancement

When the conditions for detecting proteins by ammoniacal silver staining (B. R. Oakley, D. R. Kirsch, and N. R. Morris (1980) Anal. Biochem. 105, 361-363.) following gel electrophoresis were varied, it was noted that glutaraldehyde pretreatment was necessary for maximal staining, which could not be explained simply as the result of "fixation." Further studies indicated that glutaraldehyde enhancement of protein staining with this silver reagent was probably due to oxidation of the aldehyde groups by silver ions, resulting in metallic silver depositions within the gel which act as nucleation sites for additional metallic silver localization in the protein bands upon the addition of formaldehyde developer. This proposed mechanism is consistent with the Tollen's reaction, as well as some aspects of the photographic process. Consistent with this notion, silver-staining intensities are directly related to mole percentage lysine of various standard proteins.

Fast and slow chicken skeletal muscles contain different alpha and beta tropomyosins

Avian tropomyosin has been purified from fast skeletal muscles (breast muscle and posterior latissimus dorsi : PLD) and from a slow skeletal muscle (anterior latissimus dorsi : ALD) and the alpha and beta subunits have been further separated using preparative gel electrophoresis. These subunits have been subjected to partial proteolysis using different proteolytic enzymes. In this communication we show that this procedure allows to distinguish not only between fast and slow alpha tropomyosin but also between fast and slow beta tropomyosin. Furthermore we have raised an antiserum against the fast alpha tropomyosin and we present evidence to show that this antiserum does not cross-react with the slow alpha tropomyosin. These results are taken to indicate that all these tropomyosin subunits represent different gene products.