A functional copy of the ptx operon with its promoter was generated by insertion of the ptx-ptl terminator next to the S3 gene. The five structural genes of PT (modified Caspase inhibitor S1, S2, S4, S5, and S3) with its operon promoter were amplified from Bp-WWC DNA using the primers PtxF-BamHI and PtxR-MCS. The 3469 bp amplified product was digested with BamHI and SpeI and the recovered fragment was ligated into pSKΔRI cut with the same enzymes to yield pSKptx. Plasmid pSKΔRI is a variant of pBluescript

II SK + where the EcoRI site has been removed by digestion and filled-in with the Klenow enzyme and re-circularized. The ptx-ptl operon terminator was then amplified with the TerF-EcoRI and TerR-SpeI primers. The 223 bp product was HDAC phosphorylation doubly digested with EcoRI and SpeI and ligated into pSKptx cut with the same enzymes. After transformation and colony selection, the resulting plasmid was designated as pSKptxter (Figure 3C). This plasmid was then doubly digested Wnt inhibition with BamHI and SpeI and ligated into pSSPD5Cm3 cut with the same enzymes to yield the conjugative vector pSSPDptxter. Allelic exchange into Bp-PD53Cm was performed as described above with replica screening for SmS and CmS colonies to obtain the strain designated as Bp-WWD. The integration of S1 mutated

gene at the designated position was confirmed by PCR with specific primers. The primers could bind the upstream 5′ (5′FPD-int and R-R9K primers), 3′ (F-E129G and 3′RPD-int primers) downstream flanking regions, and internal S1 gene. Insertion of a second copy of the prn structural gene Integration of a chloramphenicol resistance gene into the target site selected for integrating a second copy of the PRN structural gene A derivative of pBluescript SK + lacking the BamHI site was constructed by digestion with the enzyme,

filling-in with the Klenow enzyme, and ligation. The resulting plasmid was transformed into E. coli and designated as pSKΔH1. The sequence of the B. pertussis Tohama strain was scanned and pseudo-genes were identified. The DNA sequence (posn. 1345693) between a putative exported dehydrogenase (posn. 1344710-1345685) and a putative aspartate racemase pseudo-gene (posn. 1345693-1346049) was selected as the insertion site. These two genes carried frameshift mutations and were not functional (Figure 5A). The 5′-upstream Phosphoglycerate kinase region to the targeted insertion site was amplified using primers carrying SpeI (5′F-PD2-SpeI) and a multilinker including BamHI and NotI (5′R-PD2-MCS) restriction sites. The amplified product was isolated by gel electrophoresis and doubly digested with SpeI and NotI. The resulting fragment was ligated into a fragment of pSKΔH1 which was digested with the same enzymes. The resulting plasmid was transformed into E. coli and designated as pSKPD25. The 3′-downstream fragment was similarly amplified with primers carrying XbaI(3′F-PD2-XbaI) and NotI (3′R-PD2-NotI) restriction sites.