B. Selleck C646 fragilis C10 proteases genes, bfp1 and bfp4, are co-transcribed with those for predicted Staphostatin-like inhibitors For both the streptococcal and staphylococcal systems, the proteases and adjacently encoded inhibitors are co-transcribed [13, 28]. To determine if this transcriptional coupling of protease and inhibitor genes was also

present in B. fragilis, RNA was isolated from broth grown 638R cells, and analysed by reverse transcriptase PCR, using a series of specific primers for the protease and inhibitor genes (Table 4). Amplicons were detected for all C10 protease structural genes suggesting that all the proteases were transcribed in vitro (Fig. 4, Lanes 2, 6, 7 and 8 for bfp1, bfp2, bfp3 and bfp4 respectively). Amplification of a 1.9 Kb product (Fig. 4, Lane 5) using primers Bfi1A_F and Bfi1B_R supports the hypothesis that bfp1 is co-transcribed Thiazovivin solubility dmso on a single mRNA with bfi1A and bfi1B. In addition, amplification of a 1.65 Kb product with primers Bfp4_F and Bfi4_R suggests that bfp4 is transcriptionally coupled to bfi4 (Fig. 4, Lane 9). Table 4 Oligonucleotide primers used in this study. Primer Sequence Commenta Bfp1_F CAGCAGCATATGGACGAAGAAATCATTATTTTGATTAAT E, L Bfp1_R CAGCAGGGATCCTTACCACAAAATTTCAGTTCCC E, L Bfp2_F CAGCAGCATATGACAAGAAGAGTTGATTCTGCCAG this website E Bfp2_R CAGCAGGGATCCTTATTTATTAGGTGACACTTTAAT

E Bfp3_F CAGCAGGGATCCAGAAGATAATGTAATTGCTTCTTT E Bfp3_R CAGCCAGGAATTCTCATCGGTGTATATTGGTTATC E Bfp4_F CAGCAGGGATCCGAAGACAATTTAGAATCTTTAA E, L Bfp4_R CAGCAGGGATCCTCATCGCGATATAATAGAATATTC E Bfi1A_F CAGCAGGAATTCGAGGATGTAATGGCTATTATG E, L Bfi1A_R CAGCAGGGATCCTTACCTTCCAATATAAATGTC E Bfi1B_F CAGCAGGGATCCACACCAACCAGATACTCCACC E Bfi1B_R CAGCAGGAATTCTTACTCTTTTTTTTCGGCTGTG E, L Bfi4_F CAGCAGGAATTCAGGGATGGAGATTGGGATTC E Bfi4_R CAGCAGGGATCCTTAATTATCCTTTCCCTTTTGTTT E, L Bfgi2_Int_F CCTGATATTAGCTTCTCTATCTTTTTTGCC

I Urocanase Bfgi2_Int_R CAGCAGGGATTCCGAAGATAATGTAATTGCTTC I Bfgi2_attB_F CCGGGAATGTTTCGTCAGGAATTGATGGTG I Bfgi2_attB_R GGTTTATTGATTGTTATTTGTCGGCAAAG I a Primer used in E = Expression studies, L = Linkage studies, I = Integration/Excision studies Figure 4 Analysis of expression and transcriptional coupling of bfp genes in Bacteroides fragilis. Horizontal open arrows represent the protease (white) and putative inhibitor (grey) genes. Small filled black arrows represent the positions of the oligonucleotide primers used in the reverse-transcription PCR analysis, the size of the expected amplicon is given in bp between the appropriate sets of pimers. The resulting PCR fragments are presented in the right-hand panels, above which the size markers are indicated. bfp3 and bfp4 are located on genome insertions As mentioned above, two of the protease genes (bfp3 and bfp4) were identified only in strain 638R enabling a comparison with the two other sequenced strains of B. fragilis. Using the Artemis comparison tool [29], alignment of the B. fragilis NCTC9343 and B.