Supplementary Table 1. Primers used in this study.

Primer / Primer (or probe) sequence / Accession No.
Used in DECAL
5s rRNA / 5’-GGAAGCTAAGCCTGCCAGCGCCGATGATAC-3’ / Y08453
16s rRNA / 5’-TGCGGGCGATACGGGCAGACTAGAGTACTG-3’ / NC_008596
23s rRNA / 5'-TTTTGAAGAATGAGCCTGCGAGTCAGGGAC-3' / NC_008596
Uniamp primer / 5'-CCTCTGAAGGTTCCAGAATCGATAG-3 / PMCID23765*
Uniamp XhoI adapter
Top strand / 5'-CCTCTGAAGGTTCCAGAATCGATAGCTCGAGT-3' / PMCID23765*
Uniamp XhoI adapter Botttom strand / 5'-P-ACTCGAGCTATCGATTCTGGAACCTTCAGAGGTTT-3' / PMCID23765*
T7 promoter / 5'-TAATACGACTCACTATAGGG-3' / X52325
Used in real-time PCR
MSMEG_5007 / Forward
Reverse
Probe / 5’-GGATGCTGCCACCTTGGA-3’
5’-GCCCGGACTGGTCAACA-3’
5’-FAM-CCGCCACCAACTCGTC-MGB-3’ / NC_008596
MSMEG_4420 / Forward
Reverse
Probe / 5’-CCCGGGTCACGCAGT-3’
5’-CCTGAGATCACGTAAGCCATGA-3’
5’-FAM-ACCACCATGCGAAGTC-MGB-3’
MSMEG_0615 / Forward
Reverse
Probe / 5’-CGCACCTGCTGCTCGA-3’
5’-GGGCGACCTGGAACTTCAC-3’
5’-FAM-CTCGCCGAATTCATC-MGB-3’
MSMEG_0119 / Forward
Reverse
Probe / 5’-GGGATAGGCCGGCGG-3’
5’-GCGACGAAGGCGAGTTCTT-3’
5’-FAM-TTCGTGGCGTGTACCC-MGB-3’
MSMEG_3623 / Forward
Reverse
Probe / 5’-TCGCCGCCCGACTC-3’
5’-GATCGACGATCTGATCGAGATGAAC-3’
5’-FAM-CTCGACCTCATCCTCG-MGB-3’
MSMEG_3404 / Forward
Reverse
Probe / 5’-CGATCTTGTGGATGCGTTCATG-3’
5’-CGCGGTGTGCTGACC-3’
5’-FAM-CCCAGCCGGTCTCG-MGB-3’
MSMEG_4537 / Forward
Reverse
Probe / 5’-ACTGGTCAACAACCCCGAATAC-3’
5’-AGCGCGTCGAGATCGT-3’
5’-FAM-ACGCCCGAGCAGACCA-MGB-3’
MSMEG_5355 / Forward
Reverse
Probe / 5’-GTTTACGCCCGGAACATTCAC-3’
5’-GGCCGTCAATGTGCCTGA-3’
5’-FAM-TTCACCGCCGGAACAT-MGB-3’
MSMEG_5356 / Forward
Reverse
Probe / 5’-CGGGTGTACTGGCGATCAA-3’
5’-CGGTGCAGGCGATTTTCAC-3’
5’-FAM-CAGCCACACCAACGTC-MGB-3’
MSMEG_6615 / Forward
Reverse
Probe / 5’-CGTGACGGATCGCCATGT-3’
5’-GCTGCCAAACGCCAATCTC-3’
5’-FAM-AAGGCCGCAGAACAA-MGB-3’
MSMEG_2515 / Forward
Reverse
Probe / 5’-GCTGATCGTCGAACTGCTCTAC-3’
5’-CCGCGAGGTGTCGATGT-3’
5’-FAM-TCGAGCCCGCACAACT-MGB-3’
MSMEG_4515 / Forward
Reverse
Probe / 5’-CGCGACGGCCAATGC-3’
5’-GCCCTGATCGGGTCGAA-3’
5’-FAM-CCTACGCCGAACTGC-MGB-3’
gyrA / Forward
Reverse
Probe / 5’-CTCGACATCGACGACATCCA-3’
5’-CTGCGCAGCTGCATGT-3’
5’-FAM-CCCAGGCGATCCTC-MGB-3’

* The nucleotide sequences for the Uniamp primer, Uniamp XhoI adapter Top strand, and Uniamp XhoI adapter Bottom strand are referred to paper in the ‘DECAL’ section of Methods.


Supplementary Table 2. Mycobacterium smegmatis genes specifically induced during intracellular survival in THP-1 macrophages.

Gene / Gene product / Fold
THP-1
MSMEG_6267 / thiocyanate hydrolase gamma subunit / 4
MSMEG_6268 / putative ScnB protein / 4
MSMEG_0993 / histidine kinase / 2.6
MSMEG_6208 / palmitoyl-CoA hydrolase / 2.3
MSMEG_4526 / hypothetical protein / 1.8
MSMEG_5473 / transporter / 1.8
MSMEG_4525 / putative oxygen-independent coproporphyrinogen III oxidase / 1.8
MSMEG_5472 / 5,10-methenyltetrahydrofolate synthetase / 1.8
MSMEG_2611 / mycothione/glutathione reductase / 1.8
MSMEG_1091 / urease accessory protein UreE / 1.6
MSMEG_6620 / 539 bp at 3' side: hypothetical protein / 1.6
MSMEG_5908 / acyl-CoA synthetase / 1.6
MSMEG_1090 / amidase / 1.6
MSMEG_6617 / 611 bp at 5' side: nudix hydrolase / 1.6
MSMEG_5877 / hypothetical protein / 1.6
MSMEG_5878 / serine esterase, cutinase family protein / 1.6
MSMEG_5938 / hypothetical protein / 1.5
MSMEG_5935 / ATP-dependent DNA helicase / 1.5


Supplementary Table 3. List of the functional categories of induced genes identified in this study.

Functional category / No. of induced genes
A-SMS / D-SMS
Translation / 0 / 1
Transcription / 2 / 0
Replication, recombination, and repair / 5 / 1
Defense mechanisms / 1 / 0
Signal transduction mechanism / 0 / 1
Cell wall/membrane biogenesis / 1 / 0
Posttranslational modification, protein turnover, chaperones / 3 / 1
Energy production and conversion / 5 / 1
Carbohydrate transport and metabolism / 4 / 1
Amino acid transport and metabolism / 7 / 1
Coenzyme transport and metabolism / 1 / 2
Lipid transport and metabolism / 4 / 2
Inorganic ion transport and metabolism / 3 / 0
Secondary metabolites biosynthesis, transport, and catabolism / 1 / 0
General function prediction only / 3 / 0
Function unknown / 2 / 0
Not in COGs / 16 / 7
Total / 58 / 18

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