The ripX Locus of Bacillus subtilis Encodes a Site-Specific Recombinase Involved in Proper Chromosome Partitioning

Abstract

The Bacillus subtilis ripX gene encodes a protein that has 37 and 44% identity with the XerC and XerD site-specific recombinases of Escherichia coli. XerC and XerD are hypothesized to act in concert at the dif site to resolve dimeric chromosomes formed by recombination during replication. Cultures of ripX mutants contained a subpopulation of unequal-size cells held together in long chains. The chains included anucleate cells and cells with aberrantly dense or diffuse nucleoids, indicating a chromosome partitioning failure. This result is consistent with RipX having a role in the resolution of chromosome dimers inB. subtilis. Spores contain a single uninitiated chromosome, and analysis of germinated, outgrowing spores showed that the placement of FtsZ rings and septa is affected in ripXstrains by the first division after the initiation of germination. The introduction of a recA mutation into ripXstrains resulted in only slight modifications of the ripXphenotype, suggesting that chromosome dimers can form in a RecA-independent manner in B. subtilis. In addition to RipX, the CodV protein of B. subtilis shows extensive similarity to XerC and XerD. The RipX and CodV proteins were shown to bind in vitro to DNA containing the E. coli dif site. Together they functioned efficiently in vitro to catalyze site-specific cleavage of an artificial Holliday junction containing adif site. Inactivation of codV alone did not cause a discernible change in phenotype, and it is speculated that RipX can substitute for CodV in vivo.

Bacterial Chromosome Segregation

“…The rate of nicking is, however, low and is not thought to be of any biological importance (18). Homologs of XerC and XerD have been described from a number of organisms, including Pseudomonas aeruginosa (55), Salmonella typhimurium (44), B. subtilis (125,132), and several species of Enterobacteriaceae (131), which suggests that this mechanism of dimer resolution is highly conserved.…”

Xer Site-Specific Recombination: Promoting Vertical and Horizontal Transmission of Genetic Information

“…1(A), [10,11,12]). In addition to E. coli, chromosome dimer resolution has been studied in several Bacteria, including Bacillus subtilis, Campylobacter jejuni, Caulobacter crescentus, Haemophilus influenzae, Helicobacter pylori, Lactococcus lactis, Staphylococcus aureus, Vibrio cholerae, and Xanthomonas campestris, and in two Archaea, Pyrococcus abyssi and Sulfolobus solfataricus (13,14,15,16,17,18,19,20,21,22,23,24,25,26). Evidence of its importance for the fitness of cells has been directly obtained in B. subtilis, C. crescentus, E. coli, H. pylori, S. solfataricus, and V. cholerae (13,14,15,16,17,27,28,29).…”

Interaction of the putative tyrosine recombinases RipX (UU145), XerC (UU222), and CodV (UU529) ofUreaplasma parvumserovar 3 with specific DNA

“…Other family members related to the k-Int, such as the Flp from the yeast 2l plasmid, the XerC/D of Escherichia (E.) coli, the Cre recombinase of phage P1, the HvsR of Mycoplasma (M.) pulmonis, and the Xer1 of M. agalactiae, function in the amplification/maintenance of plasmid copy number (Hoess et al, 1984), the elimination of chromosome dimers from replicated chromosomes (Hayes & Sherratt, 1997), the cyclization of virion DNA and the life cycle of temperate phages (Sternberg et al, 1986), the alteration of the type I restriction modification system and of cell-surface components (Sitaraman et al, 2002), and in phase variation of membrane proteins (Czurda et al, 2010), respectively. In E. coli, the proteins XerC and XerD (CodV and RipX in Bacillus subtilis) act in concert at a sequence designated dif 'deletion-induced filamentation' to resolve dimeric chromosomes after chromosome replication (Blakely et al, 1991(Blakely et al, , 1993Sciochetti et al, 1999Sciochetti et al, , 2001. The dif site is usually a 28-nucleotide motif associated with the chromosome's replication terminus and serves as template for chromosome dimer resolution.…”