Asymmetric template function of microbial deoxyribonucleic acids: transcription of ribosomal and soluble ribonucleic acids

Differential responses of Bacillus subtilis rRNA promoters to nutritional stress

The in vivo expression levels of four rRNA promoter pairs (rrnp(1)p(2)) of Bacillus subtilis were determined by employing single-copy lacZ fusions integrated at the amyE locus. The rrnO, rrnJ, rrnD, and rrnB promoters displayed unique growth rate regulation and stringent responses. Both lacZ activity and mRNA levels were highest for rrnO under all growth conditions tested, while rrnJ, rrnB, and rrnD showed decreasing levels of activity. During amino acid starvation induced by serine hydroxamate (SHX), only the strong rrnO and rrnJ promoters demonstrated stringent responses. Under the growth conditions used, the rrn promoters showed responses similar to the responses to carbon source limitation induced by α-methyl glucoside (α-MG). The ratio of P2 to P1 transcripts, determined by primer extension analysis, was high for the strong rrnO and rrnJ promoters, while only P2 transcripts were detected for the weak rrnD and rrnB promoters. Cloned P1 or P2 promoter fragments of rrnO or rrnJ were differentially regulated. In wild-type (relA(+)) and suppressor [relA(S)] strains under the conditions tested, only P2 responded to carbon source limitation by a decrease in RNA synthesis, correlating with an increase in (p)ppGpp levels and a decrease in the GTP concentration. The weak P1 promoter elements remain relaxed in the three genetic backgrounds [relA(+), relA, relA(S)] in the presence of α-MG. During amino acid starvation, P2 was stringently regulated in relA(+) and relA(S) cells, while only rrnJp(1) was also regulated, but to a lesser extent. Both the relA(+) and relA(S) strains showed (p)ppGpp accumulation after α-MG treatment but not after SHX treatment. These data reveal the complex nature of B. subtilis rrn promoter regulation in response to stress, and they suggest that the P2 promoters may play a more prominent role in the stringent response.

In vitro transcription from Bacillus subtilis nucleoids by homologous RNA polymerase

The effect of DNA structural features on RNA synthesis was investigated. Purified Bacillus subtilis nucleoids templated from vegetative cells were transcribed by the homologous RNA polymerase using Hg-UTP as one of the nucleotide substrates. Low RNA polymerase/DNA ratios were used during transcription in order to avoid nonspecific initiations. The rate of synthesis of total RNA was 40% greater on nucleoid templates than on naked DNA. The proportion of asymmetric transcript synthesized on nucleoid templates (HvsL strand transcripts) was close to that observed in vivo, whereas with naked DNA this value was at least 3-times lower. The percentage of rRNA relative to the total RNA, synthesized in the in vitro system with the nucleoid template, approaches the rate of the in vivo transcription. The size of the RNA synthesized on nucleoids was large and heterogeneous while with naked DNA it was homogeneous and of about 6 S. Our results suggest that the supercoiled, folded nucleoids may retain some of the structural features responsible for the regulation of RNA synthesis in vivo.

Asymmetric distribution of exogenous thymidine among pyrimidine isostichs suggests compartmentalization of replicative DNA synthesis during regeneration in rat liver

The distribution of radioactivity among pyrimidine isostichs (or isoplyths) of DNA from 24-h regenerating rat liver was studied with [3H]Thd, [14C]orotate or with inorganic 32Pi. Expression of incorporated radioactivity as log10% of total radioactivity recovered for each of the 11 pyrimidine isostichs detected showed that radioactivity from [3H]Thd was asymmetrically distributed among the isostichs, i.e., 3H radioactivity failed to access regions of DNA yielding lower molecular weight pyrimidine isostichs as efficiently as it accessed regions yielding higher molecular weight pyrimidine isostichs. The thymine (T) content of isostichs exceeded that of cytosine (C), i.e., T/C ratios for the first 10 isostichs averaged 1.43 +/- 0.08 and 1.28 +/- 0.05, depending on the method of analysis; furthermore, the T/C ratio for isostich 1 was significantly higher than ratios for isostichs 2 through 10. Asymmetric distributions of [3H]Thd radioactivity also were seen at 18 or 30 h post-partial hepatectomy. Thus, radioactivity from [3H]Thd, a DNA precursor from the salvage pathway, failed to efficiently access lower molecular weight isostichs despite thymine enrichment, suggesting that thymine moieties were supplied from additional sources. Radioactivity from [14C]orotate accessed lower molecular weight pyrimidine tracts more efficiently than [3H]Thd, but less efficiently than it accessed higher molecular weight isostichs, resulting in an asymmetric distribution of 14C radioactivity. This result suggested that appreciable quantities of thymine and cytosine moieties utilized for DNA synthesis were supplied de novo, but other sources also were utilized. Radioactivity from 32Pi, a de novo precursor, was distributed symmetrically, i.e., the slope among lower molecular weight isostichs increased enough that it was indistinguishable from slopes for intermediate and higher molecular weight isostichs. Since 32P radioactivity among lower molecular weight isostichs reflects appreciable contributions of de novo phosphate moieties from both pyrimidine- and purine-containing deoxynucleoside triphosphates, opportunities for observing contributions of 32P radioactivity from pathways other than the de novo pathways appeared to lie beyond limits of detectability. The distribution of radioactivity from labeled DNA precursors among lower molecular weight pyrimidine tracts (a) indicate that thymine moieties are contributed by both salvage and de novo pathways; (b) support the possibility that cytosine moieties also are contributed by both pathways; and (c) support the 'replitase' concept for channeling dNTPs to replicating forks.

Asymmetric transcription during post-germinative development of Bacillus subtilis spores

The relative transcription from L and H strands of Bacillus subtilis DNA during consecutive stages of spore outgrowth was determined and compared to the transcription pattern during log-phase growth of vegetative cells. Pulses of [3H] uridine were administered during early, middle and late outgrowth phases of germination and the RNAs isolated. The asymmetry ratio of H/L as determined by hybridization at saturating RNA/DNA inputs showed a gradual decrease. During the period studied (10-90 and 90-160 min post-induction), about 50 and 35%, respectively, of the radioactive RNA consisted of ribosomal RNA transcripts. The decrease in the H/L asymmetry ratio was due predominantly to the appearance and accumulation of L strand transcripts and not to either changes in the quantity of H strand transcripts nor to fluctuation in the rate of rRNA synthesis.

New transfer ribonucleic acid species during sporulation of Bacillus subtilis

The transfer ribonucleic acid (tRNA) populations from log-phase cells, sporulating cells (stage III), and dormant spores were compared by tRNA-deoxyribonucleic acid hybridization techniques. New tRNA species not found in log-phase cells were observed in stage III cells. Some of the tRNA made during sporulation were also present in dormant spores. Although the role and function of these new tRNA species cannot be ascribed directly to the sporulation process, their presence indicates that new tRNA genes can be transcribed during sporulation and suggests that translational control may be exerted during sporulation by tRNA.

Messenger ribonucleic acid of dormant spores of Bacillus subtilis

Evidence of the presence of messenger ribonucleic acid (mRNA) in dormant spores of Bacillus subtilis has been obtained. The bulk RNA from spores was isolated and labeled in vitro with tritiated dimethyl sulfate. The spore RNA hybridized to 2.4 to 3.2% of the B. subtilis genome. The RNA hybridized to both the complementary heavy and light fractions of deoxyribonucleic acid (DNA). Bulk RNA from log-phase cells competed with virtually all the spore RNA for the heavy DNA fraction and with part of the spore RNA for the light DNA fraction. Bulk RNA from stage IV cells in sporulation also competed with all of the spore RNA for the heavy DNA fraction and with essentially all the spore RNA for the light DNA fraction. These results indicate that dormant spores contain mRNA species present in both log-phase cells and stage IV cells of sporulation. The RNA polymerase in the developing forespore must be able to recognize promotor sites for both log-phase and sporulation genes.

Transcription from the complementary deoxyribonucleic acid strands of Bacillus subtilis during various stages of sporulation

The messenger ribonucleic acid (mRNA) pattern of log-phase and sporulating cells of Bacillus subtilis has been analyzed by deoxyribonucleic acid (DNA)-RNA hybrid studies with the complementary-strand fragments of DNA. Approximately 80% of the mRNA of log-phase and sporulating cells from stages I, III, and IV hybridizes with the heavy DNA fragments, and 20% hybridizes with the light DNA fragments. Hybrid competition studies indicated that there was either a greatly reduced rate of transcription or a turn-off of some log-phase genes during the sporulation stages. However, a significant amount of log-phase gene transcription occurred even at late stages of sporulation. Similar studies indicate a significantly increased rate of transcription or a turn-on of sporulation phase genes during the latter stages of sproulation. There is a sequential increase in the amount of sporulation-specific transcription from both complementary-strand fragments of DNA. These results indicate that the RNA polymerase population in sporulating cells can transcribe both log-phase and sporulation-phase genes.

Chromatographically fractionated complementary strands of Bacillus subtilis deoxyribonucleic acid: biological properties

Biological, physical, and chromatographic properties of methylated albuminkieselguhr (MAK)-fractionated complementary strands, designated as light (L) and heavy (H), of Bacillus subtilis deoxyribonucleic acid (DNA) are presented. The pattern of transforming activity along the MAK elution profile of alkilidenatured DNA shows that the residually active molecules selectively fractionated ahead of the L strand fraction, whereas the most active self-annealed molecules fractionated preferentially at the trailing end of the H strand fraction. The restoration rate of transforming activity in the late-eluting H molecules was rapid and independent of concentration during the annealing reaction. The data suggest that the self-annealing activity in the H strand is due in part to the formation of intrastrand secondary structures. Hydroxyapatite chromatography of self-annealed L and H strands yielded a major fraction (I) of highly purified strand preparations devoid of transforming activity and hypochromicity, and a minor "nativelike" fraction (II). Sedimentation velocity measurements show that, in addition to the mutual complementary nature of the L and H fractions, they differ in molecular size and possibly configuration.

Chromatographically fractionated complementary strands of Bacillus subtilis deoxyribonucleic acid: transformation of hybrids

The annealing properties as measured by the restoration of transforming activity and hypochromicity of methylated albumin-kieselguhr (MAK)-fractionated complementary strands of Bacillus subtilis deoxyribonucleic acid (DNA) are presented. Temperature-absorbance measurements performed on annealed mixtures of various L and H strand fractions indicated the existence of a complementarity gradient between the two MAK peaks. The markers purA16, leu-8, metB(5), thr-5, and the linked marker hisB(2)-try-2 exhibited different bimodal distributions on MAK columns. The transforming efficiency of heteroduplex mixtures, prepared by cross-annealing resolved complementary strands of wild-type and recipient DNA, was compared. The transforming efficiency of the wild-type L and H strands was equal in one preparation and unequal in a second preparation. It was found that in the second strand preparation the heteroduplex DNA containing the H strand from wild type was more efficient for all of the markers tested. The variations in transforming efficiencies of the complementary strands in heteroduplex molecules reported here and by others are due in part to strands of unequal length and probably to the self-annealing property of the H strands. At present, no conclusion could be made regarding the existence of strand selection bias during integration of donor DNA in competent B. subtilis cells.

Distribution of pyrimidine oligonucleotides in strands L and H of Bacillus subtilis DNA

The distribution of pyrimidine oligodeoxynucleotide clusters in L and H strands of Bacillus subtilis DNA separated by methylated albumin-Kieselguhr has been determined. Preparations of native and single-stranded DNA were degraded with diphenylamine in formic acid, and the released isostichs with the general formula of Py(n)P(n+1) were separated on DEAE-cellulose by chain length. Eleven isostichs were obtained for strands L and H in unequal proportions. Each isostich fraction was subfractionated by base composition on DEAE-cellulose at pH 3.0. 61 Pyrimidine oligonucleotide clusters were separated from the H strand and only 46 from the L strand. The findings show a higher degree of asymmetry between the strands in the distribution of cytosine-rich clusters as compared with thymine-rich clusters. The longest cytosine oligodeoxynucleotide present in both strands is of chain length 5. There is an unusually high distribution of thymine oligodeoxynucleotides of length 5-11. Up to chain length 6, the distribution of thymine oligodeoxynucleotides between the strands is about equal; from chain length 7 to 11 they occur predominantly in the H strand.

In vitro synthesis of ribosomal RNA by Bacillus subtilis RNA polymerase

Two kinds of hybridization competition experiments show that Bacillus subtilis RNA polymerase synthesizes ribosomal RNA (rRNA) in vitro with B. subtilis DNA as a template. First, RNA synthesized in vitro competes with the hybridization of [(32)P]rRNA synthesized in vivo to the heavy strand of B. subtilis DNA. Second, unlabeled rRNA synthesized in vivo competes with the hybridization of [(3)H]RNA synthesized in vitro to denatured DNA or heavy-strand DNA, but not to light-strand DNA. The ability of RNA polymerase holoenzyme to synthesize rRNA in vitro is not lost after extensive purification. RNA polymerase core enzyme, however, which is missing the sigma factor, synthesizes little rRNA in vitro.RNA polymerase purified from wild-type sporulating cells synthesizes little rRNA in vitro, while the in vitro synthesis of rRNA by RNA polymerase from stationary phase cells of the sporulation-defective mutant rfr 10 is apparently unimpaired.

Asymmetric template function of microbial deoxyribonucleic acids: transcription of messenger ribonucleic acid

In Bacillus subtilis and Escherichia coli, pulse-labeled ribonucleic acid (RNA) synthesized during step-down growth hybridized preferentially with the heavy (H) strand of methylated albumin-Kieselguhr-fractionated deoxyribonucleic acid (DNA). At high RNA inputs, the ratio of RNA hybridized with the H strand to that hybridized with the light (L) strand was 8.7 for B. subtilis and 2.0 for E. coli. At high DNA inputs, the H/L hybridization ratio increased by a factor of two. This change in the hybridization ratio was attributable to the fraction of the pulse-labeled RNA which is in stable RNA components. The hybridization peak of pulse-labeled RNA was specifically located in the late-eluting region of the absorbance profile of the H strand. This region was considered to represent the most actively transcribing H strand templates.

Preferential transcription of Bacillus subtilis light deoxyribonucleic acid strands during sporulation

Messenger ribonucleic acid (RNA) from log and sporulation stages of growth were transcribed mainly from the heavy strand of the complementary strands of Bacillus subtilis deoxyribonucleic acid (DNA). During sporulation a slight transcription shift from heavy to light DNA strands was observed. RNA-DNA hybrid competition experiments revealed that this shift was due to sporulation-specific transcription from light-DNA strands.