Rolling-circle plasmids fromBacillus subtilis: complete nucleotide sequences and analyses of genes of pTA1015, pTA1040, pTA1050 and pTA1060, and comparisons with related plasmids from Gram-positive bacteria

Abstract

Most small plasmids of Gram-positive bacteria use the rolling-circle mechanism of replication and several of these have been studied in considerable detail at the DNA level and for the function of their genes. Although most of the common laboratory Bacillus subtilis 168 strains do not contain plasmids, several industrial strains and natural soil isolates do contain rolling-circle replicating (RCR) plasmids. So far, knowledge about these plasmids was mainly limited to: (i) a classification into seven groups, based on size and restriction patterns; and (ii) DNA sequences of the replication region of a limited number of them. To increase the knowledge, also with respect to other functions specified by these plasmids, we have determined the complete DNA sequence of four plasmids, representing different groups, and performed computer-assisted and experimental analyses on the possible function of their genes. The plasmids analyzed are pTA1015 (5.8 kbp), pTA1040 (7.8 kbp), pTA1050 (8.4 kbp), and pTA1060 (8.7 kbp). These plasmids have a structural organization similar to most other known RCR plasmids. They contain highly related replication functions, both for leading and lagging strand synthesis. pTA1015 and pTA1060 contain a mobilization gene enabling their conjugative transfer. Strikingly, in addition to the conserved replication modules, these plasmids contain unique module(s) with genes which are not present on known RCR plasmids of other Gram-positive bacteria. Examples are genes encoding a type I signal peptidase and genes encoding proteins belonging to the family of response regulator aspartate phosphatases. The latter are likely to be involved in the regulation of post-exponential phase processes. The presence of these modules on plasmids may reflect an adaptation to the special conditions to which the host cells were exposed.

Biochemical and Genetic Characterization of Coagulin, a New Antilisterial Bacteriocin in the Pediocin Family of Bacteriocins, Produced by Bacillus coagulans I 4

“…They display 49 to 55% similarity and 63 to 74% identity with the putative Mob product from pI 4 . It was suggested that this N-terminal part could constitute an important functional region of these proteins (34). The two conserved motifs previously described for Mob proteins (20,34) are present in the aligned sequences (Fig.…”

“…Surprisingly, comparison with the databases indicated that the deduced 474-aa protein displayed a high degree of similarity (40 to 74%) to corresponding regions deduced from mob-pre (plasmid recombination enzyme) genes present on several plasmids, which were found in strains belonging to various gram-positive genera (including Bacillus, Lactococcus, Streptococcus, Lactobacillus, Enterococcus, and Staphylococcus). In several cases, the corresponding mob genes have been shown to be required for conjugative mobilization and site-specific recombination (34). Much higher levels of identity were observed within the N-terminal parts of these proteins.…”

“…4A, boxes I and II). Motif I contains a putative DNA-binding tyrosine residue involved in DNA nicking activity (34).…”

“…The corresponding structural features of reported mobilization modules are the oriT-RS A sites, the cognate sequences recognized and nicked by the Mob proteins (17,34). The putative pI 4 oriT-RS A site could be located through alignment immediately upstream of pI 4 mob gene, as it is almost identical to corresponding sites present in plasmids encoding the Mob proteins presented Fig.…”

Bacillus Thuringiensis 68038‐71‐1

“…Similarly, the sso, type, originally isolated from Staphylococcus, is functional in multiple Gram-positive bacteria, including Bacillus strains (Boe et al, 1989). Another module often present in Gram-positive RCR plasmids is a mobilization entity that enables plasmid transmission between bacteria during conjugation ( G u z m k & Espinosa, 1997;Meijer et al, 1998). As pointed out by Ilyina & Koonin (1992), the organization and activity (DNA nicking and strand displacement) of the plasmid-transfer module are reminiscent of those of the minimal replicon, with the mobilization protein (Mob) and origin of transfer (oriT) corresponding to the Rep and dso, respectively.…”