Identification of 11 pH-regulated genes in Borrelia burgdorferi localizing to linear plasmids

When Borrelia burgdorferi is transmitted from the tick vector to the mammalian host, the bacterium experiences alterations in its environment, such as changes in temperature and pH. Previously, we observed numerous alterations in the membrane protein profile when B. burgdorferi B31 was grown at pH 7.0 compared to pH 8.0. Here we identify 11 genes localizing to linear plasmids that are up-regulated at pH 7.0 relative to pH 8.0 in vitro. Seven genes (bba03, bba24, bba64, bba66, bbe31, bbj41/bbi39 [encoding products that are 99% identical], and bbk01) were indirectly identified by proteomic analysis of membrane proteins. Another gene, bba36, was identified by screening a B. burgdorferi B31 genomic library with cross-adsorbed hyperimmune rabbit serum. Two additional genes, bba65 and bba73, were identified by Northern blot analysis. Genes bba64, bba65, bba66, bbj41/bbi39, and bba73 are members of paralogous gene family 54, and bbe31 is a member of the closely related paralogous gene family 60. Gene bba24 is part of a bicistronic operon with bba25 that encodes the well-characterized decorin binding proteins A and B. All 11 genes were transcriptionally regulated, yet the degree of pH regulation varied, with some genes more tightly regulated than others. The regions upstream of these pH-regulated genes appeared to be unrelated, yet many contained dyad repeats ranging from 12 to 25 nucleotides in length that may be involved in the regulation of these genes.