Additional file 2: Figure S2a. of Genome-wide expression profiling establishes novel modulatory roles of vitamin C in THP-1 human monocytic cell line

Fold expression values for the housekeeping genes. Heat map was generated using the fold expression values for ten housekeeping genes. Figure S2b. Raw gProcessed signal intensity values for housekeeping genes. The values shown on the Y-axis (log2 scale) are the background subtracted raw intensity values. UT, untreated; AA, ascorbic acid (vit C- treatment). The numbers in sample names refer to biological replicate numbers. (DOCX 262 kb

Additional file 3: Table S1. of Genome-wide expression profiling establishes novel modulatory roles of vitamin C in THP-1 human monocytic cell line

Target gene expression of regulatory genes enriched in class ‘Regulation of gene expression’ at 8 h. (DOCX 95 kb

Genome analysis identifies a spontaneous nonsense mutation in ppsD leading to attenuation of virulence in laboratory-manipulated Mycobacterium tuberculosis

Abstract Background A previous laboratory study involving wild type, mutant and devR/dosR complemented strains of Mycobacterium tuberculosis reported the attenuation phenotype of complemented strain, Comp1. This phenotype was intriguing since the parental strain H37Rv, devR mutant (Mut1) and additional complemented strains, Comp9 and Comp11, were virulent in the guinea pig model. Results Towards deciphering the mechanism underlying the attenuation of Comp1, a whole genome sequencing approach was undertaken. Eight Single Nucleotide Polymorphisms (SNPs) unique to the Comp1 strain were identified. Of these, 5 SNPs were non-synonymous and included a G➞A mutation resulting in a W1591Stop mutation in ppsD gene of the phthiocerol dimycocerosate (PDIM) biosynthetic cluster. Targeted sequence analysis confirmed this mutation in only Comp1 strain and not in wild type (H37Rv), devR knockout (Mut1) or other complemented (Comp9 and Comp11) bacteria. Differential expression of the PDIM locus in Comp1 bacteria was observed which was associated with a partial deficiency of PDIM, an increased sensitivity to detergent and a compromised ability to infect human THP-1 cells. Conclusions It is proposed that a spontaneous mutation in the ppsD gene of Comp1 underlies down-modulation of the PDIM locus which is associated with defects in permeability and infectivity as well as virulence attenuation in guinea pigs. Our study demonstrates the value of whole genome sequencing for resolving unexplainable bacterial phenotypes and recommends the assessment of PDIM status while assessing virulence properties of laboratory-manipulated strains of M. tuberculosis