In contrast, the Euro-African “”strain cluster C”" has a low frequency of cognate sites for RMS in cluster 1, but high for “”RMS cluster 2″” (Figure 2). The cognate sites for RMS cluster 1 have a significantly lower G + C content compared to the cluster 2 cognate sites (59.4 ± 17.4 and 91.6 ± 20.4%, respectively. T-test = 0.002). “”Strain cluster B”" includes hspEAsia as well as hpEurope and hpAfrica1
from Mestizo and African hosts and shows a mosaic profile selleck compound of the cognate recognition sites, consistent with the mosaic genetic structure shown in their MLS (Additional file 1: Figure S1). Figure 2 Heatmap of the profile for 15 RE recognition sites on MLS DNA sequences for 110 H. pylori strains. Higher and lower frequencies of the cognate recognition sites are represented by red and blue, respectively. The upper tree showed three main strainclusters: A) Includes hspAmerind Topoisomerase inhibitor (N=25), hspEAsia (N=5), and hpEurope (N=7) strains; B) Mostly hpEurope (N=21), but also hspEAsia (N=6), and hpAfrica1 (N=2) strains; and C) hpAfrica1 (N=23), and hpEurope (N=20) strains. The hpEurope strains studied were mostly recovered from Mestizo hosts. The phylogeny
on the left shows two enzyme clusters, that correlate with the A, B and C cluster-strains. Strain-specific methylase representation Differences in transformation rates might be due to differences in the frequency of cognate restriction sites, but also to variation in the protection conferred by active methylases belonging to the RMS. We tested the hypothesis that cognate restriction sites are more
protected by active methylases in hpEurope than in hspAmerind strains. Progesterone We selected 18 representative H. pylori strains; 9 were hpEurope recovered from European (n = 4), Mestizo (n = 4), and GW2580 supplier Amerindian (N = 1) hosts, and 9 were hspAmerind from Amerindian hosts (Additional file 1: Table S2). To determine methylase protection, genomic DNA from each strain was subject to digestion by each of 16 restriction endonucleases (Additional file 1: Table S3). Susceptibility to digestion indicated lack of an active methylase. The restriction results showed a range of 5–14 active methylases (average = 8.6 ± 2.6) per H. pylori strain of the 16 examined. There were non-significant differences in the number (Wilcoxon test, p > 0.05; Figure 3, Additional file 1: Table S3) or variances (F test, p > 0.05) of active methylases between hpEurope and hspAmerind strains. The only exception was the enzyme HpaII, to which DNA from the hspAmerind strains was significantly more resistant (83%) than DNA from the hpEurope strains (42%; Wilcoxon test; p < 0.05). Overall, the results confirm that H. pylori strains conserve similar active methylase protection, regardless of their population assignment. Figure 3 Total number of active methylases per strain.