Wheat embryo ribonucleates. V. Generation of N2--dimethylguanylate when 'fully sequenced' homogeneous species of transfer RNA are used as substrates for wheat embryo methyltransferases

When S-adenosly[methyl-14-C]methionine and various species of transfer RNA are used as substrates for wheat embryo methyltransferases, the principal site of guanylate-N-2 methylation can be shown to be a G-residue between the stems of the dihydrouridine and anticodon loops. This common site of guanylate-N-2 methylation is referred to as the interstem target site. 2. When the interstem target site is the non-terminal G-residue in a G-C-G-C sequence, as in the cases of Escherichia coli tRNA1-Leu, tRNA-Ile, and tRNA3-Ser, there is preponderant dimethylation to yield N-2-dimethylguanylate. 3. When the interstem target site is part of a U-C-G-U sequence, as in the case of E. coli tRNAf-Met, there is diminished dimethylation and correspondingly increased monomethylation to yield N-2-monomethylguanylate. 4. When the interstem target site is the non-terminal G-residue in an A-U-G-G sequence, as in the case of yeast tRNA-Asp, there is negligible dimethylation and almost exclusive monomethylation to yield N-2-monomethylguanylate. 5. The concerted way in which the primary, secondary, and tertiary structures of tRNA molecules might influence the efficacy of these methylations is the subject of a brief discussion. Attention is also focused on the evolutionary and molecular basis for the generally non-random distributions of methylated oligonucleotide sequences in ribosomal and transfer ribonucleates.

Regulation of RNA synthesis in Escherichia coli. III. Degradation of guanosine 5'-diphosphate 3'-diphosphate in cold-shocked cells

Cold-shocked cells of Escherichia coli can degrade intracellularly accumulated guanosine 5'-diphosphate 3'-diphosphate (ppGpp). The rate of ppGpp degradation is governed, as in whole cells, by the spoT gene; a rapid breakdown reaction is associated with the presence of the spoT+ allele and at least a five-fold slower decay occurs in spoT-minus mutants. The two degradation reactions in shocked cells display the following similarities: (i) the rates of degradation are equivalent to whole cell estimates, (ii) both require a full complement of activated amino acids, (iii) both are dependent upon supplements in the reaction mixture which stimulate the availability of energy-rich compounds and (iv) neither is inhibited by concentrations of ribosomal antibiotics which severely restrict protein synthesis. Apart from characteristic rate differences, decay of ppGpp in shocked cells derived from spoT-minus strains is discerned from spoT+ mediated decay in shocked cells by sensitivity to high concentrations of tetracycline and by manganese ion dependence.

Nucleotide specificity of stringent factor and the synthesis of analogs of guanosine 5'-diphosphate 3'-diphosphate and guanosine 5'-triphosphate 3'-diphosphate

The ribosome-dependent stringent factor reaction was found to be nonspecific with regard to the number of phosphate groups linked to the 5' position of guanosine nucleotides. Both GMP and guanosine 5'-tetraphosphate could accept a pyrophosphoryl group from ATP although at a much lower rate than GDP or GTP. Guanosine 5'-monophosphate 3'-diphosphate and guanosine 5'-tetraphosphate 3'-diphosphate were the products of these reactions. Furthermore, 3'-linked analogs of guanosine 5'-diphosphate 3'-diphosphate and guanosine 5'-triphosphate 3'-diphosphate were synthesized from the corresponding ATP analog, adenosine 5'-O-(3-thiotriphosphate). The stringent factor catalyzed reverse reaction was found to be specific for guanosine 5'-diphosphate 3'-diphosphate, and was essentially inactive to the isomeric form, guanosine 5'-diphosphate 2'-diphosphate.

Strain of Escherichia coli with a temperature-sensitive mutation affecting ribosomal ribonucleic acid accumulation

A mutant of Escherichia coli has been isolated that has a temperature-sensitive mutation that results in specific loss of ribosomal ribonucleic acid (RNA) synthesis and some reduction in messenger RNA synthesis. When the strain was grown in glucose medium at a restrictive temperature, RNA accumulation ceased, but both messenger RNA and protein synthesis continued for an extended time. Because carbon metabolism was slowed drastically when strain AA-157 was placed at the restrictive temperature, this phenotype can be compared with carbon depletion conditions present during diauxic lag. However, the phenotype of mutant AA-157 differs from shift-down conditions in that guanosine-3',5'-tetraphosphate levels are unaffected; therefore, a different site is affected. This mutant strain (AA-157) thus shows many characteristics similar to an aldolase mutant previously reported (Böck and Neidhardt, 1966). However, the mutation occurred in a different position on the E. coli genetic map, and furthermore, aldolase was not temperature sensitive in strain AA-157. In this paper we present a study of macromolecular biosynthesis in this mutant.

Purification and properties of stringent factor

The stringent factor from Escherichia coli is the product of the relA locus. It is the enzyme that catalyzes the synthesis of pppGpp and ppGpp eliciting a pyrophosphate transfer from ATP to the 3'--OH of GTP (or GDP). This protein is responsible for the synthesis of pppGpp and ppGpp in stringent strains in response to an amino acid starvation. In vitro it catalyzes the synthesis of these guanosine compounds in either a ribosome-dependent reaction that requires a particular conformation of the ribosome i.e. the presence of an uncharged tRNA recognizing a codon in the acceptor (A) site of the ribosome or in a ribosome-independent reaction at temperatures under 30 degrees in the presence of only buffer, salts, and substrates. Here we report the purification of the stringent factor to near homogeneity. It is a monomeric protein with a molecular weight of 75,000. The properties of the ribosome-independent reaction are studied and it is shown that the presence of certain acidic proteins, such as the 50 S ribosomal proteins L7 and L12 or casein, or 20% methanol or both stimulates the reaction by creating an environment that together with the low temperature further stabilizes the stringent factor.

Synthesis and turnover of basal level guanosine tetraphosphate in Escherichia coli

Cultures of escherichia coli growing exponentially in Trisacetate medium were subjected to nutritional shift-up and the pool size of guanosine 5'-3'-diphosphate-3'diphosphate (ppGpp) as well as the rates of protein synthesis and net RNA synthesis were determined. In the shift to a rich medium (glucose plus 19 amino acids plus hypoxanthine) the basal level of ppGpp falls immediately with a decay constant suggesting total inhibition of synthesis; ther is no ppGpp detectable above background for 30 to 40 min. The net rate of RNA synthesis starts to increase within 1 min of the shift-up and has reached its definite postshift value well before the pool of ppGGpp rises above background lvel. In a shift-up from Tris-acetate medium to Tris-glucose medium there is a much slower readjustment of the ppGpp pool size without the transient disappearance of the nucleotide. However, in a shift-up to Tris-acetate plus 5 amino acids, a medium which supports the same growth rate as Tris-glucose medium, a dramatic, transient drop in the ppGpp pool level was observed. Relaxed cells exhibit very similar behavior to strigent cells in the same shift-up. Our data argue strongly against an exclusive role for pGpp in regulating RNA synthesis during niutritional shift-up. The kinetic data of [3H]guanosine uptake into GTP and ppGpp pools were analyzed to determine the rate of pGpp synthesis. This rate was found to be similar during expotential growth in either Tris-acetate medium. During a shift-down from Tris-glucose to Tris-acetate medium the rate of ppGpp syntesis fell by a factor of 1.5 to 2 and the turnover rate is reduced 6- to 8-fold, suggesting that the expansion in the ppGp pool during shift-down canot be due to derepression of synthesis.

Stringent control of ribosomal protein gene expression in Escherichia coli

The regulation of the expression of ribosomal protein genes was examined during partial inhibition of tRNA aminoacylation in isogenic rel(+) and rel(-) strains of E. coli B carrying a temperature-sensitive mutation in valyl-tRNA synthetase (EC 6.1.1.9) gene. Measurements of the differential synthesis rate of ribosomal protein, alpha(r) (ribosomal protein synthesis rate/total protein synthesis rate), indicate that ribosomal protein synthesis is regulated directly or indirectly by availability of charged tRNA, and that the synthesis of ribosomal protein, like the synthesis of rRNA, is subject to the influence of the rel gene control system.

A new relaxed mutant of Escherichia coli with an altered 50S ribosomal subunit

A new relaxed mutant called rel C has been isolated from a rel A(+)/rel A(+) partial diploid strain. The rel C mutant is unable to synthesize ppGpp or pppGpp in vivo in response to amino acid starvation or in vitro, but can synthesize these nucleotides in a shift-down. Rel C maps near rif. Studies in vitro demonstrate the lesion to be probably in one of the 50S ribosomal proteins that can be removed by 1.0 M LiCl.

A new transfer RNA fragment reaction: Tp psi pCpGp bound to a ribosome-messenger RNA complex induces the synthesis of guanosine tetra- and pentaphosphates

The tetranucleotide TpPsipCpGp, when bound to Escherichia coli 50S ribosomal subunits, can replace intact tRNA in the stringent factor-directed synthesis of guanosine tetra- and pentaphosphates. The TpPsipCpGp-dependent fragment reaction has a strict requirement for the 50S and 30S ribosomal subunits and synthetic or natural messenger RNA.

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.

Percent charging of transfer ribonucleic acid and levels of ppGpp and pppGpp in dormant and germinated spores of Bacillus megaterium

The levels of transfer ribonucleic acids (tRNAs) specific for 14 amino acids were almost identical in dormant spores and in spores germinated from 6 to 75 min. Germinated spore tRNAs specific for all amino acids tested were between 63 and 93% charged, and there was no significant change in this value from 6 to 75 min of germination. In contrast, tRNAs isolated from dormant spores specific for nine different amino acids were almost completely(>93%) uncharged. However, some dormant spore tRNAs, i.e., those for arginine, histidine, isoleucine, and valine, showed significant (21 to 72%) levels of aminoacylation. Dormant spores contained no detectable guanosine penta- (pppGpp), tetra- (ppGpp), or triphosphate (GTP). However, these nucleotides appeared in the first minutes of germination, and thereafter all increased in parallel with a ratio of pppGpp plus ppGpp to GTP of 0.07 to 0.11, which is characteristic of unstarved vegetative cells.

Biosynthesis of the diguanosine nucleotides. II. Mechanism of action of GTP:GTP guanylyltransferase on nucleotide metabolism in brine shrimp embryos

The enzyme GTP:GTP guanylyltransferase (Gp4G synthetase) from yolk platelets of embryos of the brine shrimp, Artemia salina, catalyzes the synthesis of P1P4-diguanosine 5′-tetraphosphate (Gp4G) and pyrophosphate (PPi) from 2 equiv of GTP in a freely reversible reaction. The Michaelis constant (Km) for GTP in the forward reaction is 2.2 mM, whereas the Km for Gp4G and PPi in the reverse reaction is 1.06 mM and 0.84 mM, respectively. Also, the yolk platelet enzyme catalyzes the synthesis of P1P3-diguanosine 5′-triphosphate (Gp3G) and GTP from equivalent amounts of GDP and Gp4G. Both GDP and Gp3G inhibit the synthesis of Gp4G and the kinetic data suggest that either two enzymes are present in the Gp4G synthetase preparations or that two catalytic sites exist on one protein, one for the synthesis of Gp3G and one for the synthesis of Gp4G. Almost 80% of the Gp4G synthetase in embryos of Artemia salina is localized in yolk platelets, and a small amount of activity is found in the mitochondrial fraction.

Localization of the stringent protein of Escherichia coli on the 50S ribosomal subunit

The "stringent" protein of the ribosome, required for its synthesis of (p)ppGpp, is readily lost during zonal centrifugation. However, enough can be retained to permit its qualitative localization. It is found in native 50S subunits, runoff 70S ribosomes, and polysomes, but not in native 30S subunits. This protein, therefore, appears to be attached to the 50S moiety of the ribosome, and it may be a constant (though easily removed) component of that structure rather than a factor that joins and leaves during the ribosome cycle.