garvieae in the phylogenetic tree, and its full genome has been determined (Cho et al., 2008). Using SSH, 192 clonal libraries were generated and tested via reverse Southern blotting analysis using L. garvieae KCTC 3772T as the tester probe Alectinib in vivo and L. lactis ssp. lactis KCTC 3769T as the driver probe to eliminate false-positive clones. Twenty-seven of 192 (14%) clones carried
inserts that hybridized to the probe for the L. garvieae genome but not to that of the L. lactis genome; this percentage is much higher than those of B. anthracis (4.3%) (Kim et al., 2008) and S. oralis (5.8%) (Park et al., 2010a), but almost identical to that of S. pneumoniae (14.1%) (Park et al., 2010c). The 27 DNA signatures specific to L. garvieae are presented in Table 2. Edited sequences were analyzed using Nucleotide blast analysis. Four (CAUA05, CAUE01, CAUF64, and CAUF84) of the 27 sequences were identified as significantly homologous to sequences from other bacterial species (75%–93% identities). In part, CAUA05 and CAUE01 showed maximum identity with Bacillus thuringiensis serovar tenebrionis plasmid pBMB165 hypothetical protein Rep165 (rep165) and replication-associated proteins genes (91% identity; 1E−06 and 90% identity; 2E−05, respectively); however, the query coverage
was very low, ranging from 22% to 24%. blastx analysis of those sequences suggested that this hypothetical protein might be a transposase of the IS116//IS110/IS902 insertion sequence (IS) protein family of S. pneumoniae (81% identity; 9E−13 and 74% Dabrafenib price identity; Galeterone 2E−06, respectively). An IS is a short DNA sequence that acts as a simple transposable element. Different prokaryotic genomes contain different types of IS families; L. lactis does not seem to have
this type of IS family (Bolotin et al., 2001), suggesting that this might be a novel transposase introduced from S. pneumoniae via horizontal gene transfer. CAUF64 (GenBank accession number JM426708) showed significant identity with two neighboring genes, pyrH and rrf, of S. pneumoniae NV104 (76% identity; 2E−105). blastx analysis of those sequences showed that this hypothetical protein corresponded to part of the ribosome recycling factor (50% identity; 3E−55) and the uridine 5′-monophosphate (UMP) kinase (94% identity; 3E−54). CAUF84 (GenBank accession number JM426710) was notably matched to transposase gene sequences of Lactococcus lactis ssp. cremoris at both the nucleotide (93% identity; 5E−78) and protein levels (35% identity; 1E−23). The remaining 23 sequences had no identities with any nucleotide sequences in the current NCBI GenBank database. The whole-genome sequences of L. lactis strain subsp. lactis KF147 and CV56 have been reported (Siezen et al., 2010; Gao et al., 2011), but those of L. garvieae have not yet been completed. Thus, there is insufficient nucleotide and protein information in GenBank. Using the full genome information of L. lactis subsp. lactis IL1403 and S.