Direct fractionation of genes by preparative electrophoresis of Bacillus subtilis DNA

Size fractionation using agarose gels

In the Basic Protocol, digested genomic DNA is size fractionated on a slab agarose gel, and the appropriate region of the gel is defined by Southern blot analysis (for subgenomic libraries) or by size (for genomic libraries) and the DNA is eluted. An Alternate Protocol describes electrophoresis using a Bull's-eye apparatus. Digested genomic DNA is loaded onto a large preparative circular agarose gel in this apparatus, the DNA fragments are electrophoresed toward the center of the gel and then eluted. Fragments leaving the gel are pooled and constitute a fraction. Fractions containing the gene of interest are identified by Southern blotting of a small aliquot of alternate fractions. This procedure allows the purification of large amounts of size-fractionated DNA that is particularly well suited for genomic library construction and normally allows creation of large numbers of recombinant clones.

Genetic and physical organization of the cloned gyrA and gyrB genes of Bacillus subtilis

An 8-kilobase fragment already known to contain the gyrA gene of Bacillus subtilis was shown to encode the gyrB gene as well. Plasmids containing this fragment can rescue both B. subtilis gyrA and gyrB mutants and complement Escherichia coli gyrA mutants. Deletion analysis has indicated the gene locations on the cloned fragment. Under low-stringency conditions the cloned E. coli gyrA and gyrB genes each hybridized to the appropriate subfragments, confirming the assignment of the gene locations on the cloned DNA. In E. coli maxicells, proteins of 67,000 (gyrA) and 77,000 (gyrB) Mr were synthesized. Analysis of proteins encoded by various subfragments indicated the direction of transcription. Although the gyrA and gyrB genes are located adjacent to each other on the chromosome, they may be transcribed independently since expression of gyrA protein is not dependent upon the gyrB gene in maxicells.

Cloning the gyrA gene of Bacillus subtilis

We have isolated an eight kilobase fragment of Bacillus subtilis DNA by specific integration and excision of a plasmid containing a sequence adjacent to ribosomal operon rrn O. The genetic locus of the cloned fragment was verified by linkage of the integrated vector to nearby genetic markers using both transduction and transformation. Functional gyrA activity encoded by this fragment complements E. coli gyrA mutants. Recombination between the Bacillus sequences and the E. coli chromosome did not occur. The Bacillus wild type gyrA gene, which confers sensitivity to nalidixic acid, is dominant in E. coli as is the E. coli gene. The cloned DNA precisely defines the physical location of the gyrA mutation on the B. subtilis chromosome. Since an analogous fragment from a nalidixic acid resistant strain has also been isolated, and shown to transform B. subtilis to nalidixic acid resistance, both alleles have been cloned.

Isolation of an autonomously replicating DNA fragment from the region of defective bacteriophage PBSX of Bacillus subtilis

We have isolated a 5.4-kilobase fragment of Bacillus subtilis DNA that confers the ability to replicate upon a nonreplicative plasmid. The B. subtilis 168 EcoRI fragment was ligated into the chimeric plasmid pCs540, which contains a chloramphenicol resistance determinant from the Staphylococcus aureus plasmid pC194 and an HpaII fragment from the Escherichia coli plasmid, pSC101. A recE B. subtilis derivative, strain BD224, is capable of maintaining this DNA as an autonomously replicating plasmid. In rec+ recipients, chloramphenicol-resistant transformants do not contain free plasmid. The plasmid is integrated as demonstrated by alterations in the pattern of chromosomal restriction enzyme fragments to which the plasmid hybridizes. The site of plasmid integration was mapped by PBS1-mediated transduction to the metC-PBSX region. A strain was a deletion in the region of defective bacteriophage PBSX differs in the hybridization profile obtained by probing EcoRI digests with this cloned fragment. This same deletion mutant, though proficient in normal recombinational pathways, permits autonomous replication of the plasmid apparently owing to the lack of an homologous chromosomal region with which to recombine. We believe that, like E. coli. B. subtilis contains at least one DNA fragment capable of autonomous replication when liberated from its normally integrated chromosomal site and that this cloned DNA fragment comes from the region of defective bacteriophage PBSX.