Isolating and sequencing the infrequent 3'-ends of a specific mRNA.

Procedures are described for identification of very infrequent in vivo 3'-ends of RNA. After purification by filter hybridization, the 3'-ends were labeled with [5'-32P] cytosine-3'-P in the RNA ligase reaction. Significantly fewer counts were incorporated in the ligase reaction than in the polynucleotide kinase reaction to label 5'-ends. The incorporation was increased by increasing the RNA concentration 5-10 fold by using only one round of filter hybridization. Non-specific RNA binding could be eliminated by RNase A treatment of the filter if a great excess of denatured heterologous DNA was immobilized along with the DNA probe. Significant amounts of DNA were released when eluting the hybrid RNA from such filters. DNA inhibited the ligase reaction, while its DNase products were even more inhibitory. Treatment of the DNase products with alkaline phosphatase completely eliminated the inhibition. We detected no spurious 5'- or 3'-ends generated in the hybrid RNA by RNase A activity used to reduce the non-specific RNA. Also, RNase T1 could be used in place of RNase A to eliminate non-specific RNA binding, but about 25 times more RNase T1 (microgram/microgram) was needed. We used partial alkali digestion to sequence 3'-ends. A major (one hit) and minor (two hit) set of products were produced which could be distinguished from each other by alkaline phosphatase treatment and homochromatography of the products.

Serum factors that stimulate fatty acid oxidation: physiological specificity.

In the accompanying paper (Wice et al., 1986) we reported that serum from chickens contains small molecular weight compounds that stimulate long-chain fatty acid oxidation ten fold or more in HeLa cells. Here we show that this response is not limited to specific sera or to specific target cells. The specificity of the metabolic response to these factors was also investigated. They had no effect on the following major pathways of HeLa cell metabolism: 1) the oxidation of the medium-chain fatty acid, octanoic acid, 2) the rate of glycolysis of glucose, 3) the flux of glucose carbon through the oxidative arm of the pentose cycle, 4) the entry of pyruvate into the citrate cycle, 5) the oxidation of glutamine carbon, 6) the utilization rate of oxygen or 7) the rate of fatty acid synthesis. Furthermore, the increased oxidation of long-chain fatty acids was not a result of an increased uptake into the cells. Thus, the serum factors appear to be very specific for the oxidation of long-chain fatty acids for energy. Since carnitine also stimulates long-chain fatty acid oxidation in these cells, it seems likely that these compounds either facilitate the activity of carnitine or provide the same function--presumably the transport of long-chain fatty acid into and out of the mitochondria.

Serum factors that stimulate fatty acid oxidation: properties of factors.

Cultured heart muscle cells, but not HeLa cells, oxidize long-chain fatty acids in medium containing dialyzed serum. Addition of chicken serum dialysate (or non-dialized serum) stimulated palmitic acid oxidation by HeLa cells 10 to 20 fold. This serum activity was not eliminated by lipid extraction, ethanol or acid precipitation, alkaline phosphatase treatment, or autoclaving. About 80% was lost after any one of the following treatments: 6N HCl at 110 degrees C for 16 hr, pepsin, Dowex cation exchange at pH 3, or 1N KOH at 100 degrees C for 1 hr. Serum activity was separated into five or more peaks by gel filtration with Sephadex G-10. Each of these peak fractions was further purified by HPLC using a cyanopropyl-bonded resin. Carnitine, which is important for the transport of long-chain fatty acids into mitochondria for oxidation, also stimulated the oxidation of palmitate. However, these serum factors are not known precursors to carnitine since its immediate precursor 4-n-trimethylaminobutyrate, did not stimulate palmitate oxidation. Total carnitine, including that in acylcarnitine compounds, was approximately 15 microM in the chicken sera to give approximately 0.7 microM in the medium. Based on the fraction of total activity accountable by carnitine and fractional stability to acid, alkali, and pepsin, about 75% of the activity is from non-carnitine compounds. Only one of the factors appears to be carnitine or an acylcarnitine derivative. Several lines of evidence suggest that the other factors are peptide compounds.

Isolating and sequencing the predominant 5'-ends of a specific mRNA in cells. I. Purification by filter hybridization.

Procedures are considered for purification of a specific procaryotic RNA by successive hybridizations to DNA immobilized to nitrocellulose with special consideration of problems associated with subsequent end-labeling in the T4 polynucleotide kinase reaction. (1) Inhibitors of the kinase can be associated with the plasmid but were removed by electrophoresis of the DNA fragment through polyacrylamide. (2) Residual soluble acrylamide, contaminating the DNA and preventing its efficient retention to nitrocellulose, could be removed by DE52 chromatography. (3) Short denatured DNA required high salt (0.9 M) to bind to nitrocellulose but reannealed quickly at those salt concentrations unless applied at less than or equal to 0.3 micrograms/ml at 4 degrees C with a flow rate of 1 ml/min. (4) The kinetics of the hybrid reaction were a function of DNA length, concentration, and temperature. (5) Formamide was a more effective denaturing agent to remove hybrid RNA from the filter than either 12 M urea or 8 M guanidine-HCl, but caused significant release of DNA from the nitrocellulose as well as another potent inhibitor of the kinase reaction. The release of DNA and other kinase inhibitors was greatly reduced by eluting in boiling water.

Isolating and sequencing the predominant 5'-ends of a specific mRNA in cells. II. End-labeling and sequencing.

T4 polynucleotide kinase has been used to end-label specific RNA purified by multiple hybridizations to nitrocellulose-bound DNA. The pico moles of ends of a specific mRNA transcribed from the chromosome, even from several liters of Escherichia coli, give concentrations perhaps 2000-fold below the Km value of the kinase-RNA substrate. In such a reaction, optimal incorporation was observed with increasing ATP concentration to greater than or equal to 7 microM (greater than or equal to 15 mCi of carrier-free [32P]ATP in a 300-500 microliter reaction). The unreacted ATP (greater than 150-fold excess) could best be eliminated by multiple gel filtrations rather than by precipitation, ion exchange chromatography or dialysis. The [5'-32P]RNA was digested with T1 or pancreatic RNase and the [5'-32P]oligonucleotides separated by size in a 20% polyacrylamide gel. Oligonucleotides of a specific size were separated sufficiently by a second dimension electrophoresis on cellulose acetate. We have used partial alkali digestion in sequencing the purified oligonucleotides. As opposed to other digestions, alkali produces 5',3'-diphospho-oligonucleotides whose mobilities can differ from those of the monophosphates, e.g., much longer running times in conventional homochromatography.

Sugar-free growth of mammalian cells on some ribonucleosides but not on others.

It was shown earlier that a variety of vertebrate cells could grow indefinitely in sugar-free medium supplemented with either uridine or cytidine at greater than or equal to 1 mM. In contrast, most purine nucleosides do not support sugar-free growth for one of the following reasons. The generation of ribose-1-P from nucleoside phosphorylase activity is necessary to provide all essential functions of sugar metabolism. Some nucleosides, e.g. xanthosine, did not support growth because they are poor substrates for this enzyme. De novo pyrimidine synthesis was inhibited greater than 80% by adenosine or high concentrations of inosine, e.g. 10 mM, which prevented growth on these nucleosides; in contrast, pyrimidine synthesis was inhibited only marginally on 1 mM inosine or guanosine, but normal growth was only seen on 1 mM inosine, not on guanosine. The inhibition of de novo adenine nucleotide synthesis prevented growth on guanosine, since guanine nucleotides could not be converted to adenine nucleotides. Guanine nucleotides were necessary for this inhibition of purine synthesis, since a mutant blocked in their synthesis grew normally on guanosine. De novo purine synthesis was severely inhibited by adenosine, inosine, or guanosine, but in contrast to guanosine, adenosine and inosine could provide all purine requirements by direct nucleotide conversions.

Comparative energy metabolism in cultured heart muscle and HeLa cells.

The yields of energy from oxidation of fatty acids, glucose, and glutamine were compared in cultures of chick embryo heart muscle (heart) and HeLa cells. Aerobic energy production, as measured by oxygen utilization, was comparable in the two cell types. In media containing dialyzed sera, the rates of incorporation of fatty acids directly into lipids were similar in both cells and accounted for greater than 97% of fatty acid metabolism in HeLa cells. However, in heart cells only 45% ended in lipid, 42% in protein, and 13% was released as CO2; the latter two products probably reflect the oxidation of fatty acids to acetyl-coenzyme A (-CoA) and its subsequent metabolism in the citrate cycle. Increased serum concentration in the medium did not affect fatty acid metabolism in HeLa cultures, but resulted in greater oxidation by heart cells (greater than 100 times that by HeLa cells). The metabolisms of both glucose and glutamine were similar in heart and HeLa cells with greater than or equal to 60% of glucose carbon ending as medium lactate and only 3-5% converted to acetyl-CoA. About 25% of glutamine carbon ended as CO2 and increased utilizations with increasing serum concentrations was accountable in both cells by increased lactate from glucose and glutamate from glutamine. CO2 production (and energy) from glutamine was independent of glutamine concentration within a tenfold range of physiological concentrations. The yields of energy have been calculated. In 10% dialyzed calf serum, oxidation of glutamine carbon provided about half of the total energy in heart cells; glucose about 35-45%, with most coming from glycolysis; oxidation of fatty acid carbon provided only 5-10%. That greater than 90% of the aerobic energy comes from glutamine in both cells can account for the comparable rates of oxygen utilization. HeLa cells derived little or no energy from fatty acids.