Fig. 2

(A) Whole genome phylogenetic analysis based on reads from Comas et al.,⁶ identifying NCG as a member of the Manila clade of the Lineage 1 (L1) strains. Arrow denotes NCG. Gold star indicates emergence of shared C175T variant common to all L2, L3, and L4 strains. Scale bar indicates substitutions per variant as described in Saelens et al..⁵⁴

(B) Amino acid alignment of EsxM for Mtb and other mycobacterial species, noting the early stop codon in modern strains predicted to truncate the protein and eliminate C-terminal secretion sequences (boxed area).

(C) Quantitative RT-PCR analysis showing mean transcript levels of esxM and paralogs relative to sigA in WT M. marinum cultured in vitro and upon THP-1 infections (2 dpi) and in vivo larval zebrafish (4 dpi) infections. Log phase culture and phosphate starvation?error bars represent SD, data pooled from two independent experiments with three technical replicates for each. THP-1 and in vivo infection error bars represent SEM, data pooled from three independent experiments with three technical replicates. One-way ANOVA with Dunnett?s multiple comparisons test.

(D) Mean transcript levels of esxM paralogs relative to esxM in Mtb NCG and H37Rv strains cultured in vitro in 7H9 media and upon mouse infection. Bacterial RNA isolated from C57BL/6J mouse lungs at 6 wpi after i.v. infection with Mtb NCG or H37Rv strains. Error bars represent SEM, three independent experiments with three technical replicates each. Statistical comparison by one sample t test. ****p < 0.0001.

See also Figures S1 and S2 and Tables S1, S2, and S3.