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et al., 2004, 2005) and with estimates of gene expression levels in Saccharomyces cerevisiae (Kang et al., 2000) and E. coli (Young and Bremer, 1975). The highest transcript abundance was located for cag26 and for cag25. Given that cag26 encodes an effector protein, CagA, secreted by means of the sort IV secretion program, and cag25 encodes a virB2 ortholog that is believed to encode a pilin protein that types a multimeric structure (Andrzejewska et al., 2006), it can be not surprising that these genes are highly expressed. While generally, the expression amount of genes on the cag PAI was comparable across the three strains analyzed, there's some variation that seems to take place within the operons predicted by these experiments (Figure 2). We reasoned that adjacent genes transcribed with ORFs within the very same path, with the presence of intergenic transcript, may possibly represent a single transcriptional unit, specifically if the transcript abundance was equivalent across genes. For that reason, we initially regarded as the possibility that the following may perhaps represent cag PAI operons (numbered in the direction of transcription): SB-480848 Autophagy cag1-4, cag10-5, cag11-12, cag16-17, cag21-18, and cag25-22 (Figure 1). However, there were in some cases marked variations in transcript abundance of genes inside these putative operons (e.g., cag2522, Figures 1 and 2). This could take place due to differential decay of the transcript or possibly because the gene is a part of a lot more than a single transcriptional unit. To address these possibilities, we deleted the genomic area instantly upstream of your translational get started in the initially gene in each of six putative operons in H. pylori strain J166, a region most likely to include the promoter, and then measured cag PAI gene transcript abundance. We reasoned that deletion of this area need to decrease the expression degree of all genes within the transcriptional unit, and leave others unchanged. Deletion with the putative promoter regions upstream of cag1, cag10, cag11, cag16, cag21, and cag25 had differential effects on the expression of downstream genes when when compared with the isogenic wild form H. pylori J166 strain (Figure 3). Deletion of your region upstream of cag1 reduced expression of cag1-3 by three orders of magnitude and cag4 by only 1.5 orders of magnitude. By contrast, expression of cag5, a gene transcribed inside the opposite direction of this putative operon, remained basically unchanged. Deletion in the region upstream of cag10 decreased expression of each cag10 and cag9 by similar levels and had no impact on expression of cag8-7. Deletion in the putative promoters upstream of cag11, cag16, and cag21 decreased expression of the downstream genes, cag11-12, cag16-17, and cag21-18, but in every single case to diverse levels, ranging from 1 to three orders of magnitude (Figure 3). Lastly, deletion with the area upstream of cag25 decreased expression from the downstream genes cag25-23 to distinct levels and had no effect on the expression of cag22. In some instances, these benefits make clear predictions about operon structure. For example, our original prediction of cag10-5 and cag25-22 as operons was incorrect, because in every single case one or more downstream genes did notFrontiers in Cellular and Infection Microbiologywww.frontiersin.orgApril 2012 | Volume 2 | Post 46 |Ta et al.Helicobacter pylori cag PAI operon mapFIGURE 2 | Composite gene expression (mRNA copies/cell, normalized to 16S rRNA) for every gene around the cag PAI of H.