TABLE 3.

Genes repressed by RpoS in Borrelia burgdorferi in vitro and within DMCs.

¹Corresponding genome location for respective genes in strains B31 and 297. ²Lipoprotein localization for strain B31 orthologs based on Zuckert et al. (2004) and/or previously published reports. P_IM, periplasmic leaflet of inner membrane; P-OM, periplasmic leaflet of the outer membrane. ³Values are for the WT vs. ΔrpoS comparisons. Highlighting is used to indicate genes that were repressed by RpoS at least 3-fold in DMCs with adjusted p (q) value < 0.05 in WT vs. ΔrpoS mutant comparison and rpoScomp vs. ΔrpoS mutant comparisons. ⁴Closest match in strain 297 based on pairwise BLAST-P. Proteins sharing > 90% identity and located on similar genetic elements were considered orthologous. Dots (.) indicates genes for which no clear ortholog could be identified in strain 297. ⁵RpoS-repression of bb0240 in strain 297 has been confirmed previously by qRT-PCR. ⁶Sequences for bba03 and bba74, located near the telomeric regions of lp54, are missing from the strain 297 genome sequence file used for mapping. bba74 has been shown previously to be repressed by RpoS in strain 297 as well as B31 (Caimano et al., 2007; Mulay et al., 2009; Dunham-Ems et al., 2012). ⁷ospB in strain 297 contains a verified frameshift and was excluded as a pseudogene during mapping. ⁸cp9 is missing in the low-passage, virulent strain 297 isolated used for these analyses. This small circular plasmid is unstable and readily lost in vitro. Thus, the large folds of regulation observed for cp9-encoded genes in strain B31 could be due to plasmid loss rather than RpoS-mediated repression.