Kinetics of phosphate incorporation into adenosine triphosphate and guanosine triphosphate in bacteria

Electron spray ionization mass spectrometry and 2D 31P NMR for monitoring 18O/16O isotope exchange and turnover rates of metabolic oligophosphates

A new method was here developed for the determination of (18)O-labeling ratios in metabolic oligophosphates, such as ATP, at different phosphoryl moieties (α-, β-, and γ-ATP) using sensitive and rapid electrospray ionization mass spectrometry (ESI-MS). The ESI-MS-based method for monitoring of (18)O/(16)O exchange was validated with gas chromatography-mass spectrometry and 2D (31)P NMR correlation spectroscopy, the current standard methods in labeling studies. Significant correlation was found between isotopomer selective 2D (31)P NMR spectroscopy and isotopomer less selective ESI-MS method. Results demonstrate that ESI-MS provides a robust analytical platform for simultaneous determination of levels, (18)O-labeling kinetics and turnover rates of α-, β-, and γ-phosphoryls in ATP molecule. Such method is advantageous for large scale dynamic phosphometabolomic profiling of metabolic networks and acquiring information on the status of probed cellular energetic system.

Measurement of Microbial Nucleic Acid Synthesis and Specific Growth Rate by PO(4) and [H]Adenine: Field Comparison

We compared two radiotracer methods for measuring total microbial nucleic acid synthesis and specific growth rate. Using a sample from an oligotrophic environment, we found that there was excellent agreement between the two methods.

Distribution of 5'-triphosphate termini on the mRNA of Escherichia coli

We have determined the distribution of 5'-nucleoside triphosphates on the RNA in Escherichia coli. These groups represent the initial nucleoside triphosphate incorporated when RNA polymerase initiates transcription. It was estimated that at least 15% of polysome-associated messengers had triphosphates. This was interpreted to mean that removal of the triphosphate or messenger leader is not necessary for the functioning of most mRNAs but that a substantial amount of messenger processing occurs in the polysome pool. We found that the ratio of GTP- to ATP-initiated messengers was about 2 to 1. Since prior work has indicated that G- and A-initiated RNAs decay at the same rate and since a compilation of messenger start sites shows an A preference, this value implies that there is a significant physiological selection of G-initiated transcripts. We also characterized the 5'-terminal groups on RNAs in other fractions. A small amount was found associated with 30S ribosomes, presumably in initiation complexes; such complexes have not previously been detected in situ. In addition, it was concluded that the 5' terminus of rRNA precursors is processed more rapidly than is implied by the current literature.

The 5' ends of bacterial RNA. II. The triphosphate-terminated ends of primary gene transcripts

Bacterial RNA, Pulse labeled with 32Pi, was digested with pancreatic RNAase. Oligonucleotides containing a triphosphate group at the 5'-hydroxyl, and therefore derived from the original beginning ends of the RNA transcripts, were purified by hydroxyapatite chromatography and analyzed by two-dimensional paper electrophoresis. A broad diversity of species was found, although the distribution among these species was not completely uniform. Possible methods of utilizing these methods in combination with in vitro synthetic techniques are discussed.

The 5'-termini of bacterial RNA. I. The monophosphorylated termini

A two-dimensional fingerprint technique is described which separated oligonucleotides by length and number of phosphates present at the termini. The diversity of terminal nucleotide sequences was found to be quite restricted in bacterial 4-5 S RNA: in the strain used here the predominant dinucleotide species was pG-C, and the only trinucleotides produced were pG-G-Up and pG-G-Cp. Examination of total pulse-labeled RNA revealed the same restricted set of terminal trinucleotides.

Apparent average length of the transcriptional unit in bacteria

The kinetics of radioactive phosphate incorporation into the adenosine and guanosine nucleoside triphosphate termini of bacterial ribonucleic acid (RNA) was studied. Knowledge obtained in a previous investigation of the kinetics of phosphate incorporation into their precursors, adenosine 5'-triphosphate and guanosine 5'-triphosphate, allowed calculation of the average half-lives of these termini, which were found to be approximately 170 s at 21.5 C for both. The ratio between the number of nucleotides incorporated into the interior of RNA chains per second and the number of termini synthesized per second was calculated by several methods and found to be between 4,000 and 8,000. Assuming that the initiation of synthesis of a RNA chain by deoxyribonucleic acid-dependent RNA polymerase always produces a triphosphate termini and that some termini do not have half-lives so short as to not be seen in this study (less than 10 s), this is the apparent average length of the transcriptional unit. The implication of these findings to the genetic organization of transfer RNA genes is discussed.