To determine

the identity of the protein(s) contained within the 40 kDa band identified, this region (from both the BamA and the ML323 order control Thio elutions, Figure 3 lanes 4 and 5, respectively) were subsequently excised, trypsin-digested, and subjected to LC-MS/MS analysis. After MASCOT database search, the unknown protein from the BamA co-IP was identified as a 349-residue polypeptide encoded by the B. burgdorferi ORF bb0028. This protein was not identified in the band extracted from the Thio co-IP elution, suggesting that it co-immunoprecipitated specifically with BamA. Similar to BB0324, computer analyses of the BB0028 protein indicated that it contains a signal peptide with a consensus signal peptidase

II lipoprotein modification and processing site, suggesting that BB0028 is also a B. burgdorferi lipoprotein. Interestingly, BlastP analyses failed to identify any BB0028 conserved domains or any significant protein matches outside of the Borrelia genus. Figure 3 SDS-PAGE analysis of anti-BamA co-IP elutions. Cultures of B. burgdorferi strain B31 MI (2 × 1010 organisms per sample) were washed and solubilized, and the protein-containing cell lysate was used for co-immunoprecipitation (co-IP) experiments using anti-Thio and anti-BamA polyclonal antibodies. Lanes 1-4 of the Coomassie-stained SDS-PAGE gel shows the 40 kDa region from elutions of anti-BamA co-IP experiments using ATM/ATR targets increasing amounts (5 μL, 10 μL, 20 μL, or 40 μL) of antibody (titration selleck compound indicated by grey triangle). An unknown protein that was enriched Carnitine palmitoyltransferase II with increasing amount of anti-BamA antibody is indicated at left (arrow). A sample from the anti-Thio elutions (from which 40 μL antibody was used for co-IP) is shown in lane 5. To determine if BB0324 (the putative BamD ortholog) and BB0028 are BAM accessory proteins that specifically associate with BamA,

we performed anti-BamA, anti-BB0324, and anti-BB0028 immunoprecipitation experiments (Figure 4; antibodies used for immunoprecipitation assays are listed above panels). The immunoprecipitation assays were then subjected to immunoblot analysis with specific antibodies to BamA, BB0324, and BB0028 (indicated at left of panels). As shown in Figure 4, B. burgdorferi BamA co-immunoprecipitated BB0324 and BB0028. Additionally, BB0324 antibodies co-immunoprecipitated BamA and BB0028 while BB0028 antibodies co-immunoprecipitated BamA and BB0324 (Figure 4). However, none of the three proteins were detected in the Thio co-immunoprecipitation experiment control sample (Figure 4, left lane of each panel). Additionally, when immunoprecipitated proteins from all experiments were probed with antibodies to Lp6.6, which is a lipoprotein known to be localized to the inner leaflet of the borrelial OM [54], there was no detectable co-immunoprecipitation of Lp6.6 (Figure 4, bottom panel). The Lp6.