On the biosynthesis of cerebrosides containing non-hydroxy acids. 1. Mass spectrometric evidence for the psychosine pathway

[1, 1, 1′, 2′, 3′, 4′, 5′, 6′, 6′-²H₉]1-O-(β-galactopyranosyl) DL-sphinganine and [4, 5-³H₂]1-O-(β-D-galactopyranosyl) D-sphinganine^∗ were prepared, and the conversion to cerebroside of a mixture of these compounds was studied with rat brain microsomes. The product was characterized by thin layer radiochromatography in several solvent systems and, as the trimethylsilyl ether derivative, by gas-liquid chromatography — mass spectrometry. The mass spectrometric analyses conclusively showed that the glycosidic bond of the substrate remained intact during the transformation to cerebroside.     

In vitro polyoma DNA synthesis: Involvement of RNA in discontinuous chain growth

Short fragments of DNA (5 S) isolated by denaturation from polyoma replicative intermediates pulse-labeled in vitro were shown to have RNA covalently attached by three criteria: (1) such fragments were slightly denser than bulk viral DNA. (2) They could be labeled directly with α-³²P-labeled ribotriphosphates. (3) Alkaline hydrolysis of fragments labeled with α-³²P-labeled deoxynucleoside triphosphates showed ³²P transfer to 3′ ribonucleoside monophosphates. Except for a preference of transfer from dC, the link showed little sequence specificity. The data are compatible with the notion that all short fragments in replicating viral DNA are initiated by an RNA primer. This RNA is maximally 30 bases long and is rather short-lived.     

Identification of the 64 kilodalton chloroplast stromal phosphoprotein as phosphoglucomutase

Phosphorylation of the 64 kilodalton stromal phosphoprotein by incubation of pea (Pisum sativum) chloroplast extracts with [γ-³²P]ATP decreased in the presence of Glc-6-P and Glc-1,6-P₂, but was stimulated by glucose. Two-dimensional gel electrophoresis following incubation of intact chloroplasts and stromal extracts with [γ-³²P]ATP, or incubation of stromal extracts and partially purified phosphoglucomutase (EC 2.7.5.1) with [³²P]Glc-1-P showed that the identical 64 kilodalton polypeptide was labeled. A 62 kilodalton polypeptide was phosphorylated by incubation of tobacco (Nicotiana sylvestris) stromal extracts with either [γ-³²P]ATP or [³²P]Glc-1-P. In contrast, an analogous polypeptide was not phosphorylated in extracts from a tobacco mutant deficient in plastid phosphoglucomutase activity. The results indicate that the 64 (or 62) kilodalton chloroplast stromal phosphoprotein is phosphoglucomutase.     

Structure of the linkage between adenovirus DNA and the 55,000 molecular weight terminal protein

The 5′ terminus of each complementary strand of adenovirus DNA isolated from virions is covalently linked to a protein with an apparent molecular weight of 55,000. We have determined the structure of the protein-DNA linkage. The 55,000 M_r protein, linked to a small [³²P]oligonucleotide, was isolated after DNase digestion of uniformly ³²P-labeled adenovirus 5 (Ad5) DNA-protein complex. The protein was digested with trypsin and the resulting [³²P] peptides were analyzed with the following results. (1) Acid hydrolysis released a single phosphorylated amino acid which was identified as O-phosphoserine in four separate electrophoretic or chromatographic systems; (2) treatment with snake venom phosphodiesterase yielded exclusively dAMP, dCMP and dTMP as expected (there are no guanylate residues in the first 25 nucleotides at the 5′ ends of Ad5 DNA); (3) prior treatment of the [³²P]peptide preparation with snake venom phosphodiesterase greatly reduced the yield of O-phosphoserine upon subsequent acid hydrolysis. These results suggest that Ad5 DNA is bound to the terminal protein by a phosphodiester linkage to the β-OH of a serine residue. This conclusion is supported by the finding that the DNA-protein linkage is readily hydrolyzed in alkali. In 50 mm-NaOH at 70 °C the half time for hydrolysis of the linkage is about ten minutes. After incubation of Ad5 DNA under these conditions we were able to label the 5′ termini with ³²P by sequential treatment with alkaline phosphatase and polynucleotide kinase. Digestion of the end-labeled DNA to 5′ mononucleotides yielded [³²P]dCMP. We conclude that the terminal protein is bound to Ad5 DNA by a phosphodiester linkage between the β-OH of a serine residue of the protein and the 5′-OH of the terminal deoxycytidine residue of the DNA.     

Studies on the regulation of pyruvate dehydrogenase in isolated beef heart mitochondria.

The regulation of the pyruvate dehydrogenase multienzyme complex of isolated beef heart mitochondria by a phosphorylation-dephosphorylation mechanism was investigated. From mitochondria incubated under conditions favoring either a protein kinasemediated inactivation or a phosphatase-mediated reactivation, the pyruvate dehydrogenase complex was extracted and partially purified. Incorporation of ³²P from [γ-³²P]ATP into the pyruvate dehydrogenase complex corresponded to the loss of enzymatic activity. Upon incubation of the mitochondria that were preincubated with [γ-³²P]ATP under metabolic conditions favoring the phosphatase reaction, the amount of radioactivity in the ³²P-labeled fraction decreased significantly with a concomitant increase in the pyruvate dehydrogenase activity. The estimated molecular weight of the ³²P-labeled fraction derived from the mitochondrial incubation was 41,000, corresponding to the reported molecular weight of the α-subunit of the pyruvate dehydrogenase portion of the multienzyme complex.     

An easy and rapid method for the measurement of [γ-32P]ATP specific radioactivity in tissue extracts obtained from in vitro rat heart preparations labeled with 32Pi

A rapid method for the measurement of [γ-³²P]ATP specific radioactivity in tissue extracts containing other ³²P-labeled compounds is described. The neutralized acid extract is incubated with cyclic AMP-dependent protein kinase, cyclic AMP and casein. The incorporation of ³²P into casein from [γ-³²P]ATP is measured by perchloric acid precipitation of the protein on filter paper. ³²P-Casein formation is linearly related to the specific radioactivity of the [γ-³²P]ATP. Separation of ATP from other ³²P-labeled compounds is not required for the assay. Application of this method in the evaluation of [γ-³²P]ATP specific radioactivity in two rat cardiac muscle preparations exposed to ³²P_i is demonstrated.     

Dephosphorylation of rabbit skeletal muscle glycogen synthase by phosphoprotein phosphatase and human placental alkaline phosphatase

Phosphorylation of rabbit muscle glycogen synthase by cyclic AMP-dependent protein kinase results in the incorporation of ³²P into two major tryptic peptides (P-1 and P-2) which are identified by isoelectric focusing on polyacrylamide gel. When ³²P-labeled synthase is incubated with rabbit muscle phosphoprotein phosphatase both P-1 and P-2 are hydrolyzed. Incubation of ³²P-labeled synthase with human placental alkaline phosphatase results in a specific hydrolysis of P-1. Measurement of the increase in synthase activity ratio accompanied by the dephosphorylation of P-1 with human placental alkaline phosphatase and, subsequently, of P-2 with phosphoprotein phosphatase shows that both P-1 and P-2 affect the glucose-6-P dependency of the synthase.     

Studies of the Rous sarcoma virus RNA: characterization of the 5'-terminus

The 5′ terminus of the Rous Sarcoma Viral 30-40S RNA was characterized as follows: Unlabeled RNA was treated with polynucleotide kinase and (γ-³²P) ATP. Degradation of the 5′-(³²P) RNA with alkali yielded labeled pAp while degradation with venom phosphodiesterase yielded labeled 5′-AMP. Dephosphorylation with alkaline phosphatase was unnecessary for the RNA to accept³²P indicating the presence of 5′-OH ends. This establishes that the base at the 5′ end of Rous Sarcoma Viral 30-40S RNA is adenine.     

An easy and rapid method for the measurement of [γ-P]ATP specific radioactivity in tissue extracts obtained from in vitro rat heart preparations labeled with Pi

A rapid method for the measurement of [γ-³²P]ATP specific radioactivity in tissue extracts containing other ³²P-labeled compounds is described. The neutralized acid extract is incubated with cyclic AMP-dependent protein kinase, cyclic AMP and casein. The incorporation of ³²P into casein from [γ-³²P]ATP is measured by perchloric acid precipitation of the protein on filter paper. ³²P-Casein formation is linearly related to the specific radioactivity of the [γ-³²P]ATP. Separation of ATP from other ³²P-labeled compounds is not required for the assay. Application of this method in the evaluation of [γ-³²P]ATP specific radioactivity in two rat cardiac muscle preparations exposed to ³²P_i is demonstrated.     

Studies on the characterization of the sodium-potassium transport adenosinetriphosphatase. XII. Evidence for interaction of the acyl phosphate at the active site with neighboring groups

The sodium-potassium adenosinetriphosphatase (NaK ATPase), partially purified from beef brain, has been phosphorylated with [γ-³²P]ATP in the presence of Na and Mg and digested with pronase. A single ³²P-labeled peptide spot has been identified on paper electrophoresis, accounting for 60% of the radioactivity in the ³²P-labeled enzyme, the remainder of the radioactivity being [³²P]-orthophosphate resulting from breakdown of the highly labile acyl phosphate during pronase digestion. The ³²P in the pronase peptide was released as [³²P]-orthophosphate by N-propylhydroxylamine—as to be expected of an acyl phosphate compound. The pH stability of the acyl phosphate in the denatured phosphorylated NaK ATPase, in the pronase peptide and in acetyl phosphate were quite different. The phosphorylated protein had the lowest stability of higher pHs, acetyl phosphate had the highest stability, and the pronase peptide had an intermediate stability. These results indicate that the neighboring groups in the polypeptide chain containing the acyl phosphate residue influence the stability of the acyl phosphate bond.     

CVII. Total synthesis of the structural gene for an alanine transfer ribonucleic acid from yeast. Synthesis of a dodecadeoxynucleotide and a hexadeoxynucleotide corresponding to the nucleotide sequence 1 to 12

A dodecadeoxynucleotide having the sequence, d-T-G-G-T-G-G-A-C-G-A-G-T, and a hexanucleotide having the sequence, d-C-C-A-C-C-A, have been chemically synthesized. These compounds represent, respectively, the nucleotide sequence 1 to 12 of one strand and 1 to 6 of the complementary strand of the gene corresponding to yeast alanine transfer RNA. The synthesis of the dodecanucleotide started with the condensation of 5′-O-monomethoxytrityl thymidine (d-MMTr-T) with N-benzoyl-3′-O-acetyl deoxyguanosine 5′-phosphate (d-pg^BZ-OAc) to give the dinucleotide, d-MMTr-TpG^BZ. Successive condensations of suitability protected mononuoleotides with the 3′-hydroxyl end of the growing chain gave the protected heptanucleotide, d-MMTr-TpG^BZpG^BZpTpG^BZpG^BZpA^BZ. The protected heptanucleotide was then condensed with the dinucleotide, d-pC^ANpG^BZ-OAc, to give the nonanucleotide, d-MMTr-TpG^BZpG^BZpTpG^BZpG^BZpA^BZpC^ANpG^BZ. Condensation of the nonanucleotide with the protected trinucleotide, d-pA^BZpG^BZpT-OAc, gave the protected dodecanucleotide, d-MMTr-TpG^BZpG^BZpTpG^BZpG^BZ-pA^BZpC^ANpGr^BZpA^BZpG^BZpT. The condensing agents used were dicyclohexylcarbodiimide, tri-isopropylbenzenesulfonyl chloride and mesitylenesulfonyl chloride. After removal of the protecting groups, the completely deprotected dodecanucleotide was further purified by anion-exchange chromatography in the presence of 7 M-urea. The steps involved in the synthesis of the hexanucleotide were: the condensation, of 5′-O-cyanoethyl phosphate of N₍₄₎-anisoyl deoxycytidylyl-(3′ → 5′)MN₍₄₎aniaoyl deoxycytidine, d-CEpC^AnpC^An, with d-pA^BZ-OAc to give the protected trinucleotide, d-pC^AnpC^AnpA^BZ, and the condensation of cyanoethyl derivative of the trinucleotide (d-CEpC^AnpC^AnpA^BZ) with the trinucleotide, d-pC^AnpC^AnpA^BZ-OAc, to give the protected hexanucleotide, d-pC^AnpC^AnpA^BZpC^AnpC^AnpA^BZ. After removal of the N-protecting groups the 5′-phosphate group was removed by treatment with bacterial alkaline phosphatase and the hexanucleotide, d-C-C-A-C-C-A, was isolated by paper chromatography. The yields varied between 20 and 80% at different steps.     

Mechanism of DNA chain growth. XI. Structure of RNA-linked DNA fragments of Escherichia coli

The size of RNA attached to nascent DNA fragments of Escherichia coli with a chain length of 400 to 2000 nucleotides is estimated to be about 50 to 100 nucleotides from: (a) the density of the molecules of known sizes; (b) the decrease of the molecular size produced by hydrolysis with RNases or alkali; and (c) the size of RNA released by DNase treatment. Only a small decrease in molecular size is produced by RNase or alkali treatment, excluding the possibility that the RNA is located in the middle of the fragment or that ribonucleotide sequences are scattered in the molecule. The RNA is not located at the 3′ end of the molecule either, since the DNA is degraded by 3′ → 5′ exonuclease action of bacteriophage T4 DNA polymerase which has neither RNase nor DNA endonuclease activity. Positive evidence for the covalent attachment of the RNA to the 5′ end of the DNA is provided by the finding that one 5′-OH terminus of DNA is created from each RNA-linked DNA fragment by alkaline hydrolysis. The quantitative production of the 5′-OH group at the 5′ end of DNA is also found upon hydrolysis with pancreatic RNase, indicating that the 3′-terminal base of the RNA segment of the fragments is a pyrimidine. On the other hand, when the RNA-linked DNA fragments hydrolysed with alkali or pancreatic RNase are incubated with [γ-³²P]ATP and polynucleotide kinase and the DNA thus labelled is degraded to constituent 5′-mononucleotides, the ³²P is found only in dCMP. Therefore, C is the specific 5′-terminal base of the DNA segment of the RNA-linked DNA fragments, and the RNA-DNA junction has the structure … p(rPy)p(dC)p …     

Sequence analysis of small amounts of nonradioactive oligoribonucleotides containing ribose-methylated nucleosides by a combination of 3H- and 32P-labeling techniques

The oligonucleotides A-G-A-Cm-U and Gm-A-A-Y-A-ψ were used as model compounds to demonstrate how the complete nucleotide sequence of small amounts of nonradioactive oligoribonucleotides (0.2–0.3 nmol) can be derived by a combination of ³H-labeling procedures previously published and a new method for the characterization of 2′-O-methylated nucleosides based on enzymatic ³²P labeling. The newly developed method for the identification of ribose-methylated nucleosides entails ³²P labeling by [γ-³²P]ATP/polynucleotide kinase of the 5′-terminus of a ribonuclease T₂-stable 2′-O-methylated dinucleotide derived from the polyribonucleotide, conversion of the labeled dinucleotide to the ³²P-labeled 2′-O-methylated nucleoside 5′-monophosphate, and identification of the monophosphate by its chromatographic properties on a polyethyleneimine-cellulose thin layer. The novel method is simple, fast, and sensitive and, at present, represents the only way by which ribose-methylated nucleosides can be analyzed in small amounts (0.01 nmol) of nonradioactive oligonculeotides or RNA.     

Thin-layer chromatographic methods to isolate 32P-labeled 5-phosphoribosyl-alpha-1-pyrophosphate (PRPP): determination of cellular PRPP pools and assay of PRPP synthetase activity.

Conditions are described where 5-phosphoribosyl-α-1-pyrophosphate (PRPP) can be determined by thin-layer chromatographic methods commonly used for the determination of nucleoside triphosphate pools in ³²P-labeled bacteria. A two-dimensional chromatographic system is described where very small pools of PRPP (about 0.03 μmol per gram dry weight bacteria) can be determined. In a uni-dimensional chromatographic system the lower limit for detection of PRPP pools is about 0.3 μmol per gram dry weight bacteria. This uni-dimensional system offers an assay also for PRPP synthetase activity even in crude extracts using [γ-³²P]ATP as a substrate. The assay is highly specific due to the chromatographic isolation of PRPP and is very sensitive due to the use of ³²P labeling.The chromatographic methods for determination of PRPP pools and of activities of PRPP synthetase have been applied to the analysis of some mutants of Salmonella typhimurium and have provided results that agree well with the results obtained by conventional methods of PRPP analysis.     

Evidence for the involvement of a 35-kDa membrane protein in the synthesis of glucosylphosphoryldolichol

Photoactivatable (-²³P)5-azidoUDPGlc binds to two proteins in rat liver microsomes. As determined by SDS-PAGE electrophoresis, the molecular masses of the³²P-labeled proteins were found to be 62-and 35-kDa. Binding of the photoprobe to both proteins was inhibited by addition of unlabeled UDPGlc. Labeling of the higher molecular weight protein occurred in the absence of photoactivation. In contrast, formation of the³²P-labeled 35-kDa protein was dependent on exposure of the membranes to UV light (250nm). Moreover, labeling of the 35-kDa protein required the intact sugar nucleotide and divalent cations and was affected by the level of the endogenous and exogenous dolichylphosphate. All of these results are consistent with the possibility that the 35-kDa membrane protein is a component of glucosylphosphryldolichol synthase.     

Epinephrine-stimulated phosphorylation of pyruvate kinase in hepatocytes

Incubation of rat liver parenchymal cells with 10^?5m epinephrine or norepinephrine resulted in a rapid incorporation of ³²P into pyruvate kinase. Inclusion of α-adrenergic blocking agents (phenoxybenzamine or phentolamine) in the hepatocyte incubation medium prior to addition of epinephrine suppressed the subsequent phosphorylation of pyruvate kinase. On the other hand, inclusion of the β-adrenergic antagonist, propranolol, in the hepatocyte incubation medium prior to addition of epinephrine did not suppress the epinephrine-elicited phosphorylation of pyruvate kinase. Exogenous addition of either cyclic AMP or cyclic GMP to the hepatocyte incubation medium also resulted in increased phosphorylation of pyruvate kinase. To investigate whether the same amino acid residue(s) of liver pyruvate kinase was being phosphorylated in each instance, ³²P-labeled pyruvate kinase was isolated from hepatocytes after incubation in the presence or absence of either glucagon or epinephrine. In addition, purified liver pyruvate kinase was phosphorylated in vitro with a rat liver cyclic AMP-dependent protein kinase. Each ³²P-labeled pyruvate kinase was then subjected to tryptic digestion, two-dimensional thin-layer peptide mapping, and autoradiography. Each ³²P-labeled pyruvate kinase sample yielded 44 to 48 tryptic peptides upon staining with ninhydrin and 4 peptides that contain ³²P as detected by autoradiography. Furthermore, the same 4 peptides of pyruvate kinase were radiolabeled in each instance. Thus phosphorylation of pyruvate kinase in vitro with [γ-³²P]ATP or upon addition of either glucagon or epinephrine to hepatocytes incubated with ³²P_i resulted in phosphorylation of the same amino acid residues.     

A simple method for synthesizing [γ-32P]nucleoside triphosphates using [32P]acetylphosphate and acetate kinase

A simple, rapid, and inexpensive method is described for the synthesis of γ-³²P-labeled ribo- or deoxyribonucleoside triphosphates. The procedure involves chemical synthesis of [³²P]acetylphosphate and subsequent phosphorylation of nucleoside diphosphates using acetate kinase (EC 2.7.2.1) and a final purification step. The entire procedure is performed 8 h or less.     

Improved two-step method for the assay of adenylate and guanylate cyclase.

A two-step assay for adenylate and guanylate cyclase is described utilizing α-³²P-labeled ATP or GTP as substrate and involving purification of the resulting ³²P-labeled cAMP or cGMP by sequential chromatography on Dowex 50 and alumina. The Dowex 50 chromatography is performed in acid, 50 mm HCl for cGMP and 10 mm HClO₄ for cAMP, and achieves complete separation from the radiochemical impurities in the substrate which are responsible for blank. The cAMP or cGMP peaks are collected directly onto alumina columns and, under acid conditions, are completely retained by the alumina. After washing the alumina with water, the ³²P-labeled cAMP or cGMP is eluted with 0.2 m imidazole buffer and counted. The method delivers blanks amounting to .0005% of the substrate radioactivity, high recoveries, and excellent reproducibility.     

Sugar transformations associated with hexose transport in immature internodal tissue of sugar cane

After a 15 sec incubation in d-glucose-¹⁴C(U), 53–70% of the intracellular radioactivity in immature internodal tissue of sugarcane was in glucose-6-phosphate, and the remainder was in free glucose. Two unmetabolized glucose analogs, 2-deoxy-d-glucosce and 3-O-methyl-d-glucose, were transported at rates comparable to glucose but neither of these analogs was phosphorylated. Doubly-labeled d-glucose-1-¹⁴C-6-phosphate-³²P was dephosphorylated prior to deposition in the inner space, and ¹⁴C was transported into this tissue twice as rapidly as ³²P. It was also shown that ³²P in exogenously supplied glucose-6-³²P was not the source of phosphate for the intracellular synthesis of glucose-6-P. Galactose transport was similar to that of glucose in that the first major product recovered intracellularly was a phosphorylated sugar, i.e. ¹⁴C-galactose-1-P, when the tissue was incubated in d-galactose-¹⁴C(U). Although fructose, glucose, and galactose competed for transport into this tissue, free fructose and glucose predominated in the tissue extract after a 15-sce incubation in d-fructose-¹⁴C(U). This contrasted sharply, with the products of ¹⁴C-glucose transport which were comprised of phosphorylated sugars after 15 sec.