Regulated DNA rearrangement during sporulation in Bacillus weihenstephanensis KBAB4

Abstract

SummaryTemperate phages can integrate their genomes into a specific region of a host chromosome to produce lysogens (prophage). During genome insertion, prophages may interrupt the gene coding sequence. In Bacillus subtilis, the sigma factor gene sigK is interrupted by a 48 kb prophage-like element. sigK is a composite coding sequence from two partial genes during sporulation. For over two decades, however, no further examples of DNA element-mediated gene reconstitution other than sigK have been identified in spore formers. Here we report that the gene for dipicolinic acid (DPA) synthetase β subunit spoVFB in B. weihenstephanensis KBAB4 is interrupted by a prophage-like element named vfbin. DPA is synthesized in the mother cell and required for maintaining spore dormancy. We found that spoVFB was a composite coding sequence generated in the mother cell via chromosomal rearrangement that excised vfbin. Furthermore, vfbin caused excision after phageinducer treatment, but vfbin appeared to be defective as a prophage. We also found various spore-forming bacteria in which sporulation-related genes were disrupted by prophage-like DNA elements. These results demonstrate the first example of a similar mechanism that affects a sporulation gene other than sigK and suggest that this prophage-mediated DNA rearrangement is a common phenomenon in spore-forming bacteria.

Mechanism of bacterial gene rearrangement: SprA-catalyzed precise DNA recombination and its directionality control by SprB ensure the gene rearrangement and stable expression of spsM during sporulation in Bacillus subtilis

“…One plausible reason why all of the sporulation gene-intervening elements possess the LSR-encoding gene (e.g. spoIVCA in B. subtilis skin (15–18), ssrA in B. weihenstephanensis vfbin (20), Geoth_3268 in Geobacillus thermoglucosidasius (20)) may be to carry out precise gene rearrangements in a similar manner to SprA.…”

“…During sporulation, skin is excised from the chromosome to combine the ORFs in frame (14–16,18). Many other examples of sporulation-specific gene rearrangement, in addition to sigK , suggest that this phenomenon is wide-spread and common in spore-forming bacteria (20). In a previous study, we found that SPβ, an ‘active’ prophage, generates a gene rearrangement of spsM ( s pore p olysaccharide s ynthesis M) in B. subtilis strain 168 (21).…”

Large Chromosomal Rearrangements during a Long-Term Evolution Experiment with Escherichia coli

“…On shorter time scales, even single rearrangement events such as duplications, amplifications, inversions, deletions, and translocations can have profound effects on organismal phenotypes, typically by altering gene regulation or disrupting genes. In bacteria, some genome rearrangements have led to traits important for virulence (6), and rearrangements are sometimes even developmentally regulated (7). …”

Developmentally Regulated Genome Editing in Terminally Differentiated N2-Fixing Heterocysts ofAnabaena cylindricaATCC 29414

“…For heterocyst-forming cyanobacteria, these developmentally regulated genomic DNA deletions exclusively occurred in developing or mature heterocysts 22, 37 , but have not yet been observed in vegetative cells. Similarly, during sporulation, regulated genomic DNA deletions (a 42.1-kb spoVFB element and a 48-kb sigK element) occurred exclusively in mother cells of Bacillus weihenstephanensis KBAB4 and B. subtilis , but were not seen in their forespores 21, 43, 44 . Interestingly, both the heterocysts and the mother cells are terminally differentiated, non-dividing cells, unable to produce a next generation and eventually die.…”

“…Interestingly, both the heterocysts and the mother cells are terminally differentiated, non-dividing cells, unable to produce a next generation and eventually die. Therefore, the genomic DNA continuity is preserved in vegetative cells in heterocyst-forming cyanobacteria and in spores of spore-forming Bacilli 43, 44 .…”