Figure 6. The additive effect of strain-specific differences in basal in vitro gene expression and transcriptional responses to intracellular cues.

Microarray data from RNA derived from intracellular MTC 24h post-infection were compared directly following median normalization. This allows quantitative estimation of cumulative “absolute” intracellular transcript levels resulting from in vitro differences plus phagosome regulation. (A) Gene tree showing clade-specific intracellular expression levels of putative virulence factors. The narGHJI nitrate reductase operon, implicated in anaerobic nitrate respiration [84] and required for tissue-specific persistence in animal models [65], [85], is expressed at lower levels in all clade 2 versus clade 1 strains. The mce4 operon, encoding a cholesterol import system required for growth in activated macrophages and persistence in mouse lungs [30], is overexpressed in clade 2 strains. (B–D) Reduced expression of sulfolipid (SL), diacyltrehalose (DAT), and polyacyltrehalose (PAT) synthesis genes in intracellular M. africanum West African 2 strains (B) due to lower in vitro expression (B) coupled with lower induction (mmpL8, mmpL10, papA1) or repression (pks4, papA3, pks3) in phagosomes of resting macrophage (C). (E–G) Expression and regulation of DosRS dormancy regulon in MTC clinical isolates. Despite in vitro overexpression of the dosRS two-component regulator in Beijing strains, transcripts of downstream effectors were not notably elevated (E). dosRS and effectors were induced in all strains by phagosomal cues in resting (F) and activated macrophages (data not shown). Although “absolute” levels of dosRS are highest in Beijing strains, DosR-dependent genes are expressed more highly in Haarlem strains (G). Black box in genotype legend denotes reference strain CDC1551. A wider scale for gene expression (0.1–10) was used for (A,D,G).