TABLE 1.

List of the 14 DD M. tuberculosis candidate genes chosen for this study that in a prior report (20) were found downregulated or upregulated in expression in the PBS-RIF model in comparison to PBS-DMSO controls

DD M. tuberculosis candidate gene	Gene product/functiong	Functional category	Avg fold Δexpression PBS-RIF DD M. tuberculosisa,b	Avg fold Δexpression −K+ RIF DD M. tuberculosisc	Implicated in models of M. tuberculosis persistence?d	Avg CT (day 0 pooled sputum)e	Ranked expression 0–100 (day 0 sputum)f
Downregulated
icl1 (Rv0467)	Isocitrate lyase/involved in glyoxylate bypass in TCA cycle	Intermediary metabolism and respiration	−45.9h	−3.0	Yes	20.1	99.6
carD (Rv3583c)	RNA-Pol binding transcription factor	Regulatory proteins (transcriptional)	−22.0h	−1.4		21.4	99.2
vapB10 (Rv1398c)	Possible antitoxin	Virulence, detoxification, adaptation	−29.4h	−2.5	Yes	20.8	99.2
ppsA (Rv2931)	Phenol phthiocerol synthesis type I polyketide synthase	Lipid metabolism	−13.9h	−1.8	Yes	21.4	95.5
hspX (Rv2031c)	Heat shock protein (α-crystallin homolog)	Virulence, detoxification, adaptation	−10.5	1.0	Yes	20.4	92.3
Rv1738	Similar to bacterial hibernation factors	Conserved hypotheticals	−13.8	6.0	Yes	21.9	98.5
tatA (Rv2094c)	Sec-independent protein translocase	Cell wall and cell processes	−14.0	−9.7		20.6	98.1
whiB1 (Rv3219)	NO-responsive transcription factor	Regulatory proteins (transcriptional)	−11.3h	−4.2	Yes	24.0	98.6
pks15 (Rv2947c)	Probable polyketide synthase	Lipid metabolism	−16.0h	2.6		25.5	60
lldD2 (Rv1872c)	Possible l-lactate dehydrogenase (cytochrome)	Intermediary metabolism and respiration	−10.0h	−3.6	Yes	24.0	95.1
Upregulated
arsC (Rv2643)	Probable arsenic-transport integral membrane protein	Cell wall and cell processes	7.7	2.6	Yes	25.2	56.5
lpqX (Rv1228)	Probable lipoprotein	Cell wall and cell processes	17.2h	8.4		27.1	72.8
ugpC (Rv2832c)	Probable sn-glycerol-3-phosphate transport ABC transporter	Cell wall and cell processes	11.6h	9.6		25.7	32.3
rpfE (Rv2450c)	Probable resuscitation-promoting factor	Cell wall and cell processes	11.2	−2.3		27.1	32.3

^aComparing DD M. tuberculosis positive versus negative cultures from Saito et al. (20).

^bThe PBS used in this model contains potassium.

^cComparing DD M. tuberculosis positive versus negative cultures from Ignatov et al. (22).

^dTorrey et al. (23).

^eThis study.

^fWalter et al. (21) (100 represents highest expressed gene in sputum based on high-throughput qRT-PCR).

^gAbbreviations: TCA, tricarboxylic acid cycle; Pol, polymerase; NO, nitric oxide; ABC, ATP-binding cassette.

^hOther putative gene/operon family members show similar changes in expression.