176 32. PP4194 citrate synthase 2.162 33. PP0684 peptidyl-prolyl cis-trans isomerase, FKBP-type 2.077 34. PP5319 hypothetical protein 2.013 check details In order to validate the differential expression of genes observed in the
microarray experiment, semi quantitative RT PCR analysis of three genes PP_0170, PP_0233 and PP_0235, was performed as they were among genes that showed maximum up-regulation in PpoR++ strains when compared to wild type. Briefly, PP_0170 codes for a putative ABC transporter periplasmic binding protein (3.55 fold up regulation in PpoR++ strain), PP_0233, designated as tauA, encodes a putative taurine ABC transporter periplasmic binding protein (5 fold up regulation in PpoR++ strain) and PP_0235, named lsfA, codes for a putative peroxidase (3 fold up regulation in PpoR++ strain). RT PCR analysis with two independent RNA isolations shows more than two fold increases in expression of these genes in PpoR++ strain when compared to wild type and is in agreement with the results obtained in microarray (Figure 7). As these genes take part in inorganic ion utilization and oxidative stress, it is possible that PpoR might play a functional role in these processes. Figure 7 RT-PCR analysis to validate buy Vactosertib expression of genes in P. putida WCS358. Total RNA isolations were carried out from
bacterial cultures grown in minimal M9 medium using Ribopure RNA isolation kit (Ambion) and DNase treatment was carried out. cDNA synthesis was done using AMV Reverse Transcriptase (Promega) and second strand synthesis performed using Go Taq Flexi polymerase (Promega). RT-PCR analysis was performed with RNA obtained from two independent isolations and the figure shows results of one such experiment. (a) Agarose gel showing RT-PCR products for the genes PP_0170, PP_0233 and PP_0235. RT_PCR for 16S rRNA was carried out from the same RNA samples as control to ensure that equal amounts of RNA were taken. A. RT-PCR on RNA sample from P. putida WCS358 containing pBBR vector alone and B. RT-PCR on RNA sample from P. putida WCS358 containing pBBRPpoR. (b) Graph showing normalized fold difference of genes when compared to 16S rRNA expression
levels. The gel image containing bands was analyzed by Staurosporine concentration the ImageJ software and the bars indicate the fold SYN-117 ic50 increase in the intensity of the bands in PpoR++ strain (P. putida WCS358 containing pBBRPpoR) when compared to wild type (P. putida WCS358 containing pBBR vector alone). Conclusion The roles of solo QS LuxR proteins in inter-species as well inter-kingdom signaling are just beginning to be understood with a few recent studies on these proteins in non-AHL producing bacteria. The extent of the functional participation/interaction of these proteins in QS in AHL producing bacteria also differs depending on the strain. We have characterized PpoR, a solo LuxR homolog present in both AHL and non-AHL producing bacteria; its conservation indicates a significant role for this protein of P. putida.