The Bacillus subtilis ochre suppressor sup-3 is located in an operon of seven tRNA genes

Complete Genome Sequence of Bacillus subtilis Strain CU1050, Which Is Sensitive to Phage SPβ

The Gram-positive bacterium Bacillus subtilis is used as a model organism to study cellular and molecular processes. Here, we announce the complete genomic sequence of B. subtilis strain CU1050, derived from B. subtilis strain 168. CU1050 has historically been used to study suppressor mutations and phage biology, especially the lysogenic phage SPβ.

Replication initiation proteins regulate a developmental checkpoint in Bacillus subtilis

We identified a signaling pathway that prevents initiation of sporulation in Bacillus subtilis when replication initiation is impaired. We isolated mutations that allow a replication initiation mutant (dnaA) to sporulate. These mutations affect a small open reading frame, sda, that was overexpressed in replication initiation mutants and appears to be directly regulated by DnaA. Mutations in replication initiation genes inhibit the onset of sporulation by preventing activation of a transcription factor required for sporulation, Spo0A. Deletion of sda restored activation of Spo0A in replication initiation mutants. Overexpression of sda in otherwise wild-type cells inhibited activation of Spo0A and sporulation. Purified Sda inhibited a histidine kinase needed for activation of Spo0A. Our results indicate that control of sda by DnaA establishes a checkpoint that inhibits activation of Spo0A and prevents futile attempts to initiate sporulation.

Effect of host bacteria genotype on spontaneous reversions of Bacillus subtilis bacteriophage phi29 sus17 nonsense codon

Gene 17 of Bacillus subtilis bacteriophage Phi29 is an early gene playing a role in DNA replication. Its mutant sus17(112) carries the TAA nonsense triplet at the fifth codon of the gene. We isolated and sequenced 73 spontaneous revertants producing normal-size plaques on bacteria without an informational suppressor gene. In all revertants, the TAA triplet was changed by a one-base substitution and the sequences CAA, AAA, TTA, TAC and TAT were recovered at its place. The spectrum of these mutations was markedly influenced by the genotype of the bacteria in which the revertants arose. In agreement with the results described in Escherichia coli, the ratio of transversions to transitions (CAA being the only transition acceptable) was higher in strains harboring the functional allele recA(+) than in those with recA4. Our results support the idea that also in the Gram-positive B. subtilis, the spectra of spontaneous mutations are specifically modified by an SOS function. It is assumed that the single-stranded DNA chains generated in the course of phage DNA replication might act as an inducing factor.

The structure of ribonuclease P protein from Staphylococcus aureus reveals a unique binding site for single-stranded RNA

Ribonuclease P (RNaseP) catalyses the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5' terminus. The prokaryotic RNaseP holoenzyme consists of a catalytic RNA component and a protein subunit (RNaseP protein), which plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. We determined the three-dimensional high-resolution structure of the RNaseP protein from Staphylococcus aureus (117 amino acid residues) by nuclear magnetic resonance (NMR) spectroscopy in solution. The protein has an alphabeta-fold, similar to the ribonucleoprotein domain. We used small nucleic acid molecules as a model for the 5'-leader sequence to probe the propensity for generic single-stranded RNA binding on the protein surface. The NMR results reveal a contiguous interaction site, which is identical with the previously identified leader sequence binding site in RNaseP holoenzyme. The conserved arginine-rich motif does not bind single-stranded RNA. It is likely that this peptide segment binds selectively to double-stranded sections of P RNA, which are conformationally more rigid. Given the essentiality of RNaseP for the viability of the organism, knowledge of the S. aureus protein structure and insight into its interaction with RNA will help us to develop RNaseP and RNaseP protein as targets for novel antibiotics against this pathogen.

Recognition of the 5' leader and the acceptor stem of a pre-tRNA substrate by the ribozyme from Bacillus subtilis RNase P

The catalysis by the ribozyme from bacterial RNase P involves specific interactions with the structure of the tRNA substrate. Recognition of the T stem-loop by this ribozyme occurs in a groove-like structure dictated by the tertiary folding of tRNA [Loria, A., and Pan, T. (1997) Biochemistry 36, 6317]. Effects of 2'-OH --> 2'-H modifications within the acceptor stem and the 5' leader on substrate binding and catalysis are determined using a tRNAPhe substrate that is significantly cleaved at more than one site. In all but one case, the 2'-deoxy substitution has little effect on binding for cleavage at the correct and incorrect sites. Substitution of the 2'-OH group at the correct site, however, decreases the cleavage chemistry by more than 3.4 kcal/mol for cleavage at both the correct and incorrect sites. Substitutions of the 2'-OH groups at the incorrect sites have no effect for cleavage at the incorrect and correct sites. Truncation of the 5' leader results in differential effects on cleavage at different sites. These observations lead to a model in which cleavage at the correct and incorrect sites involves formation of different ribozyme-substrate complexes depending on binding of specific nucleotides in the 5' leader. Binding of the T stem-loop of tRNA and the 2'-OH group at the correct cleavage site is common for all ES complexes. An A/U-rich 5' leader significantly promotes formation of the ES complex and accelerates the cleavage chemistry over those of a C/G-rich 5' leader, but only moderately enhances cleavage at the correct site over cleavage at the incorrect sites. Since cleavage at different sites requires formation of different ES complexes, cleavage site selection can occur at the level of the ES complex and at the chemical step.

Specificity of tRNA-mRNA interactions in Bacillus subtilis tyrS antitermination

The Bacillus subtilis tyrS gene, encoding tyrosyl-tRNA synthetase, is a member of the T-box family of genes, which are regulated by control of readthrough of a leader region transcriptional terminator. Readthrough is induced by interaction of the cognate uncharged tRNA with the leader; the system responds to decreased tRNA charging, caused by amino acid limitation or insufficient levels of the aminoacyl-tRNA synthetase. Recognition of the cognate tRNA is mediated by pairing of the anticodon of the tRNA with the specifier sequence of the leader, a codon specifying the appropriate amino acid; a second interaction between the acceptor end of the tRNA and an antiterminator structure is also important. Certain switches of the specifier sequence to a new codon result in a switch in the specificity of the amino acid response, while other switches do not. These effects may reflect additional sequence or structural requirements for the mRNA-tRNA interaction. This study includes investigation of the effects of a large number of specifier sequence switches in tyrS and analysis of structural differences between tRNA(Tyr) and tRNA species which interact inefficiently with the tyrS leader to promote antitermination.

Analysis of suppressor mutations of spoIVCA mutations: occurrence of DNA rearrangement in the absence of site-specific DNA recombinase SpoIVCA in Bacillus subtilis

The spoIVCA gene of Bacillus subtilis encodes a site-specific recombinase, which excises a 48-kb skin element from the chromosomal DNA by DNA rearrangement and creates a new composite gene, sigK, on the chromosome. From spoIVCA mutants, we have isolated Spo+ revertants which have no skin element but have an intact sigK gene. This result suggests that the DNA rearrangement can occur in the absence of spoIVCA.

A CUC triplet confers leucine-dependent regulation of the Bacillus subtilis ilv-leu operon

Regulation of the ilv-leu operon probably involves interaction of a tR NA(GAG) with leader region mRNA. Conversion of a CUC (Leu) triplet located within the leader region to UUC (Phe), CGC (Arg), or UAC (Tyr) converted reporter gene expression to control by corresponding amino acids. Conversion of the CUC triplet to CUU (Leu) decreased expression and disrupted regulation. The results suggested that other tRNAs can substitute for tRNA(Leu) but that interactions in addition to pairing of the anticodon with the CUC triplet are important for proper control.

Transfer RNA gene organization and RNase P

Mature tRNAs are remarkably similar in all cells. However, the primary transcripts from tRNA genes can vary considerably due to differences in gene organization. RNase P must be able to recognize the elements that are common to all tRNA precursors to accurately remove the 5'-leader sequences.

Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA

Sequence analysis of 236 promoters recognized by the Bacillus subtilis sigma A-RNA polymerase reveals an extended promoter structure. The most highly conserved bases include the -35 and -10 hexanucleotide core elements and a TG dinucleotide at position -15, -14. In addition, several weakly conserved A and T residues are present upstream of the -35 region. Analysis of dinucleotide composition reveals A2- and T2-rich sequences in the upstream promoter region (-36 to -70) which are phased with the DNA helix: An tracts are common near -43, -54 and -65; Tn tracts predominate at the intervening positions. When compared with larger regions of the genome, upstream promoter regions have an excess of An and Tn sequences for n > 4. These data indicate that an RNA polymerase binding site affects DNA sequence as far upstream as -70. This sequence conservation is discussed in light of recent evidence that the alpha subunits of the polymerase core bind DNA and that the promoter may wrap around RNA polymerase.

Pathway of promoter melting by Bacillus subtilis RNA polymerase at a stable RNA promoter: effects of temperature, delta protein, and sigma factor mutations

Bacillus subtilis RNA polymerase (RNAP) contains a catalytic core (beta beta' alpha 2; or E) associated with one of several sigma factors, which determine promoter recognition, and delta protein, which enhances promoter selectivity. We have shown previously that specific mutations in sigma A region 2.3, or addition of delta, decrease the ability of RNAP to melt the ilv-leu promoter. Here we extend these studies to a stable RNA promoter, PtmS, which controls transcription of seven tRNA genes. KMnO4 footprinting was used to visualize DNA melting at PtmS as a function of both temperature and the protein composition of the RNAP holoenzyme. We propose that the pathway leading to productive initiation includes several intermediates: a closed complex (RPc), a complex in which DNA melting has nucleated within the conserved TATA element (RPn), and an open complex in which DNA-melting extends to at least -4 (RPo1). RNAP reconstituted with either of two mutant sigma A proteins, Y189A and W192A, was defective for both the nucleation and propagation of the transcription bubble while a third sigma A mutant, W193A, allows normal nucleation of DNA-melting, but does not efficiently propagate the melted region downstream.

tRNA genes of Streptomyces lividans: new sequences and comparison of structure and organization with those of other bacteria

Three closely linked Streptomyces lividans tRNA genes encoding two tRNA(Lys)s and a tRNA(Gly) were cloned and sequences. The structure of tRNA(Gly) is unusual for eubacterial tRNAs. Including those in previous reports (R. Sedlmeier and H. Schmieger, Nucleic Acids Res. 18:4027, 1990, and R. Sedlmeier, G. Linti, K. Gregor, and H. Schmieger, Gene 132:125-130, 1993), 18 S. lividans tRNA genes were physically mapped on the chromosome of the closely related strain Streptomyces coelicolor A3(2). The structure and organization of tRNA genes of S. lividans and S. coelicolor are compared with those of Escherichia coli and Bacillus subtilis.

Mutations in the gene for a tRNA that functions as a regulator of a transcriptional attenuator in Bacillus subtilis

It has been proposed that uncharged tRNA molecules may act as positive regulatory factors to control the expression of a number of operons in Bacillus subtilis and related bacteria by interacting with leader sequences to cause antitermination. In this study we report the isolation and characterization of regulatory mutations that modify one of the tRNA molecules predicted to have such a regulatory role. Three different alleles of the B. subtilis leucine tRNA gene leuG were found that resulted in higher expression of the ilv-leu biosynthetic operon. Each resulted in a base change in the D-loop of the leucine tRNA molecule with the anticodon 5'-GAG-3' (leucine tRNAGAG). Experiments with strains that are diploid for mutant and wild-type alleles suggested that both charged and uncharged tRNA molecules may interact with leader sequences to control expression of the operon.

Inducible amber suppressor for Bacillus subtilis

An amber suppressor variant of Bacillus subtilis tyrosyl-tRNA was constructed and placed under control of the isopropyl-beta-D-thiogalactopyranoside (IPTG)-inducible Pspac promoter. Addition of IPTG resulted in a 50-fold increase in the expression of an rpsD-lacZ fusion containing a UAG amber codon. This system permitted isolation of a conditional lethal mutant which required IPTG for growth.