Alterations in the number of rRNA operons within the Bacillus subtilis genome

Localization of rRNA synthesis in Bacillus subtilis: characterization of loci involved in transcription focus formation

In Bacillus subtilis, RNA polymerase becomes concentrated into regions of the nucleoid called transcription foci. With green fluorescent protein-tagged RNA polymerase, these structures are only observed at higher growth rates and have been shown to represent the sites of rRNA synthesis. There are 10 rRNA (rrn) operons distributed around nearly half of the chromosome. In this study we analyzed the rrn composition of transcription foci with fluorescently tagged loci and showed that they comprise the origin-proximal operon rrnO but not the more dispersed rrnE or rrnD. This suggests that transcription foci comprise only the seven origin-proximal operons rrnO, rrnA, rrnJ, rrnW, rrnI, rrnH, and rrnG. These results have important implications for our understanding of microbial chromosome structure.

Restriction fragment length polymorphism of rRNA operons for discrimination and intergenic spacer sequences for cataloging of Bacillus subtilis sub-groups

Restriction fragment length polymorphism of rRNA operons (RFLP) and 16S-23S rRNA intergenic region (ISR) sequences of Bacillus subtilis subsp. subtilis, B. subtilis subsp. spizizenii, and B. atrophaeus were compared. ISR sequences of the B. subtilis subspecies were extremely similar (W23 versus 168 rrn H, J, G,W; 96.8%; rrn D, E; 98.4%; rrnB; 97.9%) and, therefore, not useful for their differentiation. However, RFLP of rRNA operons of the B. subtilis subspecies were distinct in terms of numbers and organization within the genome (e.g. the 168 sub-group generally contained 8.3- and 8.0-kb fragments absent in the W23 sub-group). The more distantly related B. atrophaeus was distinct from both B. subtilis subspecies in terms of ISR sequence and rRNA operon number and organization. RFLP of rRNA operons discriminates the two sub-groups of Bacillus subtilis that are indistinguishable by ISR sequence. However, ISR sequence defines the relatedness of B. subtilis to other species (e.g. B. atrophaeus) within the genus Bacillus.

Variation in 16S-23S rRNA intergenic spacer regions among Bacillus subtilis 168 isolates

The genome of the Bacillus subtilis 168-type strain contains 10 ribosomal RNA (rRNA) operons. In the intergenic spacer region (ISR) between the 16S and 23S rRNA genes, five rRNA operons, rrnI-H-G and rrnJ-W, lack a trinucleotide signature region. Precise determination of molecular weight (MW), using electrospray mass spectrometry (MS), of the polymerase chain reaction (PCR) products from a segment of the ISR from the 168-type strain and B. subtilis 168-like strain 23071 demonstrated 114 and 111 basepair (bp) PCR products (due to the presence or absence of the insert in the operons) as predicted from sequence. However, PCR of the ISR segment for five other B. subtilis 168 isolates generated only a 114 bp PCR product, suggesting the presence of the trinucleotide signature region in all rRNA operons for these strains. Additional genetic variability between the seven B. subtilis 168 isolates was demonstrated by restriction fragment length polymorphism (RFLP) of the rRNA operons, with three distinct patterns found upon Southern blot analysis. The 168-type strain and three others (23066, 23067, and 23071) exhibited the same Southern pattern. Thus, operon deletion is not responsible for the absence of a 111 bp product on MS analysis for strains 23066 and 23067. Restriction analysis confirmed the presence of the trinucleotide signature region in the ISR of all rRNA operons for five B. subtilis 168 isolates; sequencing of rrnW/H from a representative strain also upheld this finding. These results help provide a better understanding of variations in sequence, operon number and chromosomal organization, both within a genome and among isolates of B. subtilis subgroup 168. It is also hypothesized that the presence of the trinucleotide insert in certain rRNA operons may play a role in rRNA maturation and protein synthesis.

Physical and genetic map of the Clostridium acetobutylicum ATCC 824 chromosome

A physical and genetic map of the Clostridium acetobutylicum ATCC 824 chromosome was constructed. The macrorestriction map for CeuI, EagI, and SstII was created by ordering the 38 restriction sites by one- and two-dimensional pulsed-field gel electrophoresis (PFGE) and by using an original strategy based on the CeuI enzyme and indirect end labelling by hybridization on both sides of the CeuI sites with rrs (16S RNA) and 3' rrl (23S RNA) probes. The circular chromosome was estimated to be 4.15 Mb in size, and the average resolution of the physical map is 110 kb. The chromosome contains 11 rrn loci, which are localized on 44% of the chromosome in a divergent transcriptional orientation regarding the presumed location of the replication origin. In addition to these 11 rrn operons, a total of 40 identified genes were mapped by hybridization experiments with genes from C. acetobutylicum and from various other clostridia as probes. The genetic map of C. acetobutylicum was compared to that of the three other endospore-forming bacteria characterized so far: Bacillus subtilis, Clostridium beijerinckii, and Clostridium perfringens. Parodoxically, the chromosomal backbone of C. acetobutylicum showed more similarity to that of B. subtilis than to those of the clostridia.

Identification and characterization of the ribosomal RNA-encoding genes in Clavibacter xyli subsp. cynodontis

Clavibacter xyli subsp. cynodontis (Cxc) is a xylem-inhabiting bacterial endophyte of Bermudagrass. This organism is classified with Gram-positive, high G + C content, coryneform-actinomycete bacteria. Southern-blot analysis showed that Cxc contains only one copy of the ribosomal RNA-encoding genes (rRNA). A clone containing the rRNA genes was isolated from a genomic library of Cxc DNA cloned in the lambda EMBL3 vector. The gene cluster was partially sequenced, revealing the gene order 5'-16S-23S-5S-3', similar to that found in other prokaryotes. Low-resolution S1 mapping suggested multiple transcription start points of the rRNA operon.

Instability of rRNA operons in Bacillus subtilis

Many laboratory strains of Bacillus subtilis contain 9 rather than 10 rRNA operons due to deletions occurring within the rrnJ-rrnW or rrnI-rrnH-rrnG gene cluster. These operons are members of two sets of closely spaced clusters located in the cysA-aroI region. Analysis of rescued DNA from integrants with insertions into rrnG and rrnH indicated that these tandemly arranged operons allowed frequent deletions of an rrn operon equivalent. These events may arise spontaneously by intrachromosomal recombination or by simultaneous double crossovers with a multimeric integrative plasmid.

Organisation of the ribosomal RNA genes in Streptomyces coelicolor A3(2)

Using Southern hybridisation of radiolabelled purified ribosomal RNAs to genomic DNA the ribosomal RNA genes of Streptomyces coelicolor A3(2) were shown to be present in six gene sets. Each gene set contains at least one copy of the 5 S, 16 S and 23 S sequences and in at least two cases these are arranged in the order 16 S - 23 S - 5 S. Three gene sets, rrnB, rrnD and rrnF, were isolated by screening a lambda library of S. coelicolor A3(2) DNA. The restriction map of one of these, rrnD, was determined and the nucleotide sequences corresponding to the three rRNAs were localised by Southern hybridisation. The gene order in rrnD is 16 S - 23 S - 5 S.

Mapping of rRNA genes with integrable plasmids in Bacillus subtilis

Integrable plasmids pGR102 and pWR103 containing ribosomal sequences from within the transcriptional units for 16S and 23S were used to transform Bacillus subtilis. To date, these plasmids integrated into 7 of 10 known rrn operons. Two such events occurred at unassigned operons, revealing a close linkage of the CAT gene of the plasmid to pha-1 situated between dal-1 and purB33 for rrnE and to thiA78 situated between glyB133 and re-12 for rrnD. All seven integration events that led to the loss of unique ribosomal BclI fragments can now be assigned to known rrn operons.