A suppressor of nonsense mutations in Bacillus subtilis

Chloramphenicol induction of cat-86 requires ribosome stalling at a specific site in the leader

The plasmid gene cat-86 specifies chloramphenicol-inducible chloramphenicol acetyltransferase in Bacillus subtilis. Induction by the antibiotic is primarily due to activation of the translation of cat-86-encoded mRNA. It has been suggested that the inducer stalls ribosomes at a discrete location in the leader region of cat-86 mRNA, which causes the destabilization of a downstream RNA secondary structure that normally sequesters the cat-86 ribosome binding site. It is the destabilization of this RNA secondary structure that permits translation of the cat-86 coding sequence. In the present report, we show that ribosomes that were stalled in the cat-86 leader by starvation of host cells for the amino acid specified by leader codon 6 induced gene expression to a level above that detected when cells were starved for the amino acids specified by leader codons 7 and 8. Starvation for amino acids specified by leader codons 3, 4, or 5 failed to activate cat-86 expression. These results indicate that the stalled ribosome that is most active in cat-86 induction has its aminoacyl site occupied by leader codon 6. To determine if chloramphenicol also stalled ribosomes in the cat-86 regulatory leader such that the aminoacyl site was occupied by codon 6, we separately changed leader codons 3, 4, 5, and 6 to the translation termination (ochre) codon TAA. Each of the mutated genes was tested for its ability to be induced by chloramphenicol. The results show that replacement of leader codons 3, 4, or 5 by the ochre codon blocked induction, whereas replacement of leader codon 6 by the ochre codon permitted induction. Collectively, these observations lead to the conclusion that cat-86 induction requires ribosome stalling in leader mRNA, and they identify leader codon 6 as the codon most likely to be occupied by the aminoacyl site of a stalled ribosome that is active in the induction.

Nucleotide sequence of the late region of Bacillus subtilis phage PZA, a close relative of phi 29

The 12,200-bp sequence of the late region of bacteriophage PZA was determined. Open reading frames (ORFs) and potential ribosome-binding sites were found in this region and the ORFs were assigned to eleven late genes. A potential bidirectional transcriptional terminator was found and its possible function is discussed.

Nucleotide sequence of the late region of Bacillus phage phi 29 completes the 19,285-bp sequence of phi 29 genome. Comparison with the homologous sequence of phage PZA

The 12,177-bp nucleotide (nt) sequence of the late region of Bacillus phage luminal diameter 29 genome was determined. This sequence completes the entire 19,285-bp sequence of phage luminal diameter 29 DNA. Eleven open reading frames were found in this region, and these were assigned to eleven late genes. Ribosome-binding sites and a potential transcriptional promoter and terminator are considered. The nt sequence was compared to the homologous region of the closely related phage PZA and tolerated variations at the nt and amino acid (aa) level were evaluated. The most frequent changes are silent nt substitutions in the third position of codons, but aa substitutions are also found.

Bacteriophage SPO1 genes 33 and 34. Location and primary structure of genes encoding regulatory subunits of Bacillus subtilis RNA polymerase

Bacteriophage SPO1 gene 33 and 34 products are required for SPO1 late gene transcription. Both proteins bind to the core RNA polymerase of the Bacillus subtilis host to direct the recognition of SPO1 late gene promoters, whose sequences differ from those of SPO1 early and middle gene promoters. We have located and cloned the genes for these two regulatory proteins, and have engineered their expression in Escherichia coli by placing them under the control of the bacteriophage lambda PL promoter. Nucleotide sequence analysis indicated that genes 33 and 34 overlap by 4 base-pairs and encode highly charged, slightly basic proteins of molecular weight 11,902 and 23,677, respectively.

Genetic location of the Bacillus subtilis sup-3 suppressor mutation

The sup-3 suppressor mutation of Bacillus subtilis has been located between the aroI and mtlB loci by PBS-1 phage transduction.

Conversion by trypsin of nonsense suppressor-produced isozymes of triosephosphate isomerase to isozymes resembling the wild type

Nonsense suppressor genes caused the synthesis of new triosephosphate isomerase isozymes in Bacillus subtilis. Incubation with trypsin produced a large decrease in the apparent molecular weight of one such isozyme and simultaneously changed the electrophoretic behavior such that it resembled that of the wild-type enzyme.

Assembly of Bacillus subtilis phage phi29. 1. Mutants in the cistrons coding for the structural proteins

The effect of mutations in the cistrons coding for the phage structural proteins has been studied by analyzing the phage-related structures accumulated after restrictive infection. Infection with susmutants in cistron 8, lacking both the major head and the fiber protein, does not produce any phage-related structure, suggesting a single route for the assembly of phage phi29; infection with ts mutants in this cistron produces isometric particles. Mutants is cistron 9, coding for the tail protein, TP1, produce DNA-free prolate heads with an internal core; these particles are abortive and contain the head proteins HPO, HP1 and HP3, the upper collar protein NP2 and the nonstructural proteins p7, p15 and p16. Mutants in cistron 10, coding for the upper collar protein, NP2, produce DNA-free isometric heads also with an internal core; they contain the head proteins and the nonstructural protein p7, suggesting that this protein forms the internal core. Mutants in cistrons 11 and 12, coding for the lower collar protein, NP3, and the neck appendages, NP1, respectively, give rise to the formation of DNA-containing normal capsids and DNA-free prolate particles, more rounded at the corners than the normal capsids and with an internal core; the DNA-containing 11-particles are formed by the head proteins and the upper collar protein; the DNA-free 11-particles contain, besides these proteins, the nonstructural protein p7 and a small amount of proteins p15 and 16. The DNA-containing 12-particles have all the normal phage structural proteins except the neck appendages, formed by protein NP1; the DNA-free particles are similar to the DNA-free 11-particles. After restricitive infection mutant sus14(1241) has a delayed lysis phenotype and produces a phage burst higher than normal, after artificial lysis. It produces DNA-containing particles, identical to wild-type phage, which have all the normal phage structural proteins, and DNA-free prolate particles, more rounded at the corners than the final phage particles and with an internal core; the last particles contain the same proteins as the DNA-free 11 or 12-particles. These particles could represent a prohead state, ready for DNA encapsulation. None of the DNA-containing particles have the nonstructural proteins p7, p15 or p16, suggesting that these proteins are released from the proheads upon DNA encapsulation.

Bacillus subtilis phage phi29. Characterization of gene products and functions

A total of 22 phi29-induced proteins have been resolved by slab gel electrophoresis; two of these proteins are the precursor and product fragment, respectively, in the synthesis of the neck appendage protein of the phage. The protein products of 10 out of the 17 cistrons detected in the genome of phage phi29 have been identified. Mutants in two other cistrons fail to synthesize two proteins. Mutants in six genes do not synthesize phage DNA. A cistron, probably involved in the final lysis of the infected bacteria, has been found. Mutants in this gene give place, under restrictive conditions, to delayed lysis and produce, after artificial lysis, a burst size similar or higher than that obtained after wild-type phage infection.

Isolation of a strong suppressor of nonsense mutations in Bacillus subtilis

By treatment of Bacillus subtilis MO-101-P spoA- met thr- su- with ethyl methanesulfonate, a strong suppressor strain of nonsense mutations, B. subtilis MO-101-P spoA- [met-]+thr- su+44, was isolated. This strain does not suppress phage phi 29 mutant susB47, selected on a B. subtilis strain containing the su+3 suppressor isolated by Georgopoulos. A revertant from this mutant, susB610, was isolated, being suppressed by both the su+3 and su+44 suppressor strains. The efficiency of suppression by strain su+44 is about 50%. The experiments shown in this paper suggest that strain su+44 contains an amber and strain su+3 an ochre suppressor.

Genetic analysis of bacteriophage phi29 of Bacillus subtilis: mapping of the cistrons coding for structural proteins

Four phage phi29 suppressor-sensitive mutants of cistron O have been examined for production of 14C-labeled viral-specific proteins in restrictive infections of Bacillus subtilis and fail to produce the protein of the viral neck lower collar. Cistrons O and F have been placed on the genetic map, containing 12 cistrons, by three-factor crosses. The phenotypes of five cistron J mutants have been analyzed by sodium dodecyl sulfate gel electrophoresis and autoradiography, and in three instances fragments of the normal polypeptide were detected. Three factor crosses with these mutants and a virus with a clear plaque phenotype were used to initiate the mapping of cistron J and the determination of the orientation of transcription in this map region.

Bacteriophages of Bacillus subtilis

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Nature of the suppressor of Bacillus subtilis HA101B

The suppressor of Bacillus subtilis HA101B is shown to act by suppression of polypeptide chain termination. The efficiency of suppression is 25 to 30%.

Viral mutation affecting bacteriophage phi 1 development in Bacillus subtilis 168

Bacillus subtilis bacteriophage phi 1m, a host-range variant, was isolated after mutagenesis of virulent bacteriophage phi 1. Unlike its wild-type antecedent, phi 1m could not form plaques on lawns of B subtilis 168 at 37 C, although it adsorbed to, penetrated, and killed this bacterium. Experiments conducted in liquid medium at 37 C showed that B. subtilis 168 cells allowed reduced levels of phi 1m development at low multiplicities of infection, whereas high multiplicity infections of this strain by the phage were abortive. Certain mutants, derived originally from B. subtilis 168, were observed to be permissive for phi 1m at 37 C; moreover, their permissive phenotype could be duplicated by growing wild-type B. subtilis 168 cells at temperatures above 47 C. Studies on phi 1m and host nucleic acid synthesis under nonpermissive conditions demonstrated that transciption and DNA synthesis proceeded up to 20 min after infection, after which time there was a cessation of all nucleic acid production. These observations are discussed with respect to other abortive bacteriophage infections in B. subtilis.