DNA strand specificity of temporal RNA classes produced during infection of Bacillus subtilis by SP82

In vitro synthesis of late bacteriophage phi 29 RNA

A crude P-100 fraction prepared from Bacillus subtilis 21 min after infection with wild-type phage phi 29 supported the in vitro synthesis of late phi 29 RNA by added RNA polymerase. Synthesis of late RNA was also detected when purified phi 29 DNA was transcribed by RNA polymerase in the presence of an S-150 fraction obtained by lysis of phi 29-infected cells in the presence of 1 M NaCl. Late phi 29 RNA was not synthesized when either the P-100 or the S-150 fraction was prepared from cultures infected with phi 29 having a mutation in gene 4.

The effect of the delta subunit on the interaction of Bacillus subtilis RNA polymerase with bases in a SP82 early gene promoter

We have examined the effect of the delta subunit on the interaction of the Bacillus subtilis RNA polymerase with an early gene promotor of phase SP82. Methylation by dimethyl sulfate, used to probe close approaches of polymerase to purines, revealed that noninitiated complexes formed by holo-enzyme (core-sigma-delta) had significantly fewer contacts than complexes formed by core-sigma. The presence or absence of delta had little or no effect on close approaches to purines in initiated complexes. DNAase I footprinting indicated that core-sigma was bound to the same region regardless of whether delta, initiating nucleotides, or both, were present. These data support the conclusion that delta acts prior to initiation to enhance promoter selectivity by limiting the number of possible interactions that the polymerase can make with DNA.

Early RNAs in SP82- and SP01-infected Bacillus subtilis may be processed

Transcription of SP82 and SP01 DNAs in vitro by Bacillus subtilis RNA polymerase yielded mostly large RNA species, with many in excess of 1,500 bases in length, whereas most of the RNAs synthesized in vivo early in infection were much smaller. Addition of an extract from uninfected B. subtilis to reaction mixtures containing RNAs synthesized in vitro generated additional discrete RNAs whose mobilities on polyacrylamide gels matched the mobilities of some of the smaller RNAs synthesized in vivo.

Analysis of bacteriophage SP82 major "early" in vitro transcripts

A restriction map was constructed for the 17.5-kilobase SalI C fragment of SP82 DNA. Unfractionated SP82 DNA, the SalI C fragment, and restriction fragments derived from SalI-C were used as templates for in vitro synthesis by the Bacillus subtilis RNA polymerase, and the resulting transcripts were analyzed by gel electrophoresis. Comparison of the RNA species obtained from SalI-C with those produced from unfractionated DNA indicated that most of the RNAs and all of the major transcripts originate from the SalI C fragment; this fragment contains one copy of the terminally redundant portion of the genome. Seven major transcripts, a bidirectional terminator site, and 5 of the 13 minor transcripts were located within the 13-kilobase redundant region. The binding of polymerase to fragments of DNA produced by digestion of SalI-C with HpaII and HhaI was used to identify promoter-bearing regions within SalI-C.

Transcription of exogenous and endogenous deoxyribonucleic acid templates in cold-shocked Bacillus subtilis

Ribonucleic acid (RNA) synthesis was examined in cold-shocked Bacillus subtilis cells. The cells were grown to mid-log stage, harvested, and cold shocked. RNA synthesis was monitored by the incorporation of [3H]uridine triphosphate or [alpha 32P]adenosine triphosphate into trichloroacetic acid-precipitable material in the presence of all four nucleoside triphosphates. The inhibition of RNA synthesis in cold-shocked cells by lipiarmycin, ethidium bromide, rifampin. or streptolydigin was analyzed using mutant or wild-type cells. Also examined were the effects of temperature, salt concentration, and the addition of polyamines or highly phosphorylated nucleotides. In ultraviolet-irradiated and cold-shocked cells, RNA wynthesis decreased to low levels. The addition of exogenous phi 29 or TSP-1 template to these cells caused a 13- to 20-fold increase in RNA synthesis, as monitored by trichloroacetic acid-precipitable counts. RNA synthesized in the presence of phi 29 deoxyribonucleic acid (DNA) hybridizes mainly to EcoRI fragments A and C of phi 29 DBA, These two fragments direct transcription by purified RNA polymerase in vitro and hybridize to early phi 29 DNA produced in vivo. Our results with TSP-1 DNA in this system indicated that the RNA produced hybridizes to the same fragments as early RNA produced in vivo. Plasmic pUB110 DNA was not transcribed in this system.

Translation of RNAs synthesized in vivo and in vitro from bacteriophage SP82 DNA

The synthesis of 69 phage-specific polypeptides during the infection of Bacillus subtilis with bacteriophage SP82 was detected by pulse-labeling, one-dimensional electrophoresis, and autoradiography. SP82 virions were found to contain approximately 22 polypeptides, most of which were synthesized late in infection; evidence was obtained for the processing of the major virion protein. RNAs extracted at different times during infection were translated by using an Escherichia coli cell-free extract. Only smaller-molecular-weight peptides were produced efficiently in vitro; in the 9,000- to 60,000-molecular-weight range, 50 to 60% of the peptides synthesized in vivo were produced by translation of RNAs extracted from infected cells. Eight of the virion peptides were produced by in vitro translation of RNAs extracted from infected cells. RNAs were synthesized under defined conditions by RNA polymerase extracted from uninfected B. subtilis and by polymerases isolated from cells 8 and 20 min after infection with SP82. Translation of these RNAs yielded characteristic and different patterns of polypeptides. Nine of the 12 polypeptides produced by translation of RNAs synthesized by the host polymerase corresponded in mobility to peptides appearing in vivo in the 0 to 3 and 3 to 6 min intervals of pulse-labeling after infection; 12 of the 25 peptides synthesized from RNAs produced by polymerase extracted 8 min after infection corresponded in mobility to peptides detected in vivo 8 min after infection, and 15 of the 22 peptides directed by RNAs made by the polymerase isolated 20 min after infection corresponded to peptides present in vivo late in infection. Five of the peptides produced in vitro from the latter RNA corresponded to virion peptides.