The transcribing strands of bacillus subtilis DNA for ribosomal and transfer RNA

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.

Defective Bacteriophage PBSH in Bacillus subtilis: III. Properties of Adenine-16 Marker in Purified Bacteriophage Deoxyribonucleic Acid

The adenine-16 (ade-16) marker (the marker nearest the chromosomal origin of Bacillus subtilis) in purified PBSH deoxyribonucleic acid (DNA) renatured more rapidly and to a greater extent than any other marker in the phage DNA, and more rapidly and to a greater extent than all markers, including ade-16, in bacterial DNA. The renaturation of the phage DNA ade-16 marker followed a first-order reaction, whereas renaturation of bacterial markers was initially a second-order reaction. No cross-linkages were detected in DNA molecules containing the ade-16 marker. Buoyant density measurements and inactivation by heat and micrococcal deoxyribonuclease of the ade-16 marker did not reveal large segments of clusters of the individual bases in these molecules. Alternative mechanisms for the unique renaturation behavior of the ade-16 marker are discussed.

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.

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.

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.

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

In Bacillus subtilis and Escherichia coli, 16 and 23S ribosomal ribonucleic acid (rRNA) hybridize exclusively with the heavy (H) strand of methylated albuminkieselguhr (MAK)-fractionated complementary deoxyribonucleic acid (DNA) strands. All the soluble RNA (4S RNA) in B. subtilis and 66 to 75% of the 4S RNA in E. coli also hybridize with the H strand. Interspecific hybridization shows that E. coli 23S rRNA also binds selectively to the DNA H strand of Salmonella typhimurium. The hybridization peak for all three cellular RNA components is specifically located in the late-eluting region of the absorbance profile of the DNA H strand. The early-eluting region of the light (L) strand preferentially inhibits the hybridization between the peak region of the H strand and 23S rRNA. These regions are considered to represent the transcribing sequences and their complements for 23S rRNA in the separated H and L strands of DNA, respectively.

Complementarity of RNA produced by enzymic transcription of native and denatured B. subtilis DNA

This paper describes the preparation and some of the properties of the RNA specimens synthesized with the aid of the RNA polymerase of E. coli by transcription of the following DNA templates: (a) undenatured B. subtilis DNA (yielding N-RNA); (b) separated strand fractions L and H isolated by chromatography of the denatured DNA on methylated albumin (yielding L-RNA and H-RNA, respectively). The study of the hybridization behavior of the various RNA products showed that N-RNA, though able to form hybrids with either strand, hybridized with H-DNA to twice as great an extent as with L-DNA. The transcripts of the separated L and H fractions exhibited complete specificity with respect to complexing: L-RNA hybridized only with L-DNA, H-RNA only with H-DNA.

Ribosomal RNA genes in bacteria: evidence for the nature of the physical linkage between 16S and 23S RNA genes in Bacillus subtilis

The nature of the arrangement of 16S and 23S ribosomal RNA genes on the Bacillus subtilis chromosome was studied by means of a Cs(2)SO(4) density gradient centrifugation technique after complexing DNA-(ribosomal) RNA hybrids with mercuric ions. It was observed that the same fragments of single-stranded DNA with an average molecular weight of 1.9 x 10(6) which hybridize with 23S RNA also hybridize with 16S RNA. This indicates that genes for both these species of ribosomal RNA are physically linked on such DNA fragments. Some evidence suggests that the two types of genes are interspersed with each other, perhaps in sets, each of which contains a 16S and a 23S ribosomal RNA gene.

Partial purification of native rRNA and tRNA cistrons from mycoplasma sp. (Kid)

Precise optical melting profiles of purified DNA from Mycoplasma sp. (Kid) show a secondary hyperchromic rise, corresponding to 1.4 per cent of the total DNA, occurring at 88 degrees C, while the bulk of the DNA melts at 79.5 degrees C, indicating an average base composition of 24.9 per cent guanine-cytosine (G-C). A method is presented, using sonication followed by hydroxyapatite column chromatography, for the partial purification of regions of a genome which contain significantly higher G-C than the average value for the genome. The procedure does not involve denaturation and renaturation of the high G-C material so that purified DNA is in its native, double-stranded state and has a normal melting profile. When applied to Mycoplasma sp. (Kid), the method yielded a fraction of native DNA enriched 40 times with respect to those regions coding for rRNA and tRNA. This enriched DNA has a saturation hybridization value of 15.9 per cent with Kid rRNA plus tRNA. The saturation hybridization values of the bulk DNA with rRNA and tRNA are 0.26 per cent and 0.16 per cent, respectively. Based on a genome size of 6.84 x 10(8), obtained by electron microscopy, this indicates that Mycoplasma sp. (Kid) contains only enough ribosomal DNA to code for one set of 23S plus 16S rRNA and only enough DNA complementary to tRNA to code for 44 different tRNA molecules.