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Table 2 The summary of transcriptomes of M. tuberculosis in sputum versus other conditions, 2021

From: Lipid droplets and the transcriptome of Mycobacterium tuberculosis from direct sputa: a literature review

Transcriptome condition

In vitro comparator

URG in sputum Mtb

DRG in sputum Mtb

Ref

SMtb vs Culture

7H10 agar /7H9 broth/Dubosa

dosR, icl1, hspX, narK2, tgs1, PE/PPE

nuoB, qcrC, and ctaD

[29]

SMtb Vs Culture

No information

Conserved Hypotheticals. mprAB: dosR is stable

pks15/1, pks10

Pks12, phoP, ESX 1-ESX-5

[89]

SMtb Vs Culture

Liquid culture

ACOD1/IRG1, GLUT1, MCT4, ESX-3, Rv0106, Rv2990c, ESX-3, mprA

TCA cycle, ETC, NADH dehydrogenase, pentose phosphate pathway (PPP), NAPDH, ROS. PhoP, small RNA mcr7, pks12, esat-6 and cfp-10, phoP

[91]

SMtb Vs Culture

MGIT 460

Glyoxylate shunt, methylcitrate cycle (icl, prpC and rv1129c), catabolism of cholesterol and fatty acids, and tgs; Nitrate reduction (narK2/3). dosR nrdZ, narK2, rv1738, pfkB, hspX, hrp1,rv3126c and rv3128c

gltA2, kgd, mdh, korA/B, sucC, rv0247c/48c, fumC and mqo), FAS-1 (fas), FAS-II, mmaA2/3/4, cmaA2, pcaA, fadD32 and pks13, NADH dehydrogenase, cytochrome C reductase

[92]

SMtb Vs culture

7H9/ DTAc

sputum and BAL had significant up-regulation of the dosR regulon

Ribosomal genes and primary metabolism genes

[93]

Day 7–14 days Vs day0

None applicable

Anaerobic respiration, PE/PPE genes, is, dosR,transcriptional factors, oxidative stress, sigma factors, toxin-antitoxin modules,

TCA cycle, ATP synthesis, ribosomal proteins, pks, ESX, replication, efflux pumps, drug-activating enzymes & drug targets

[94]

SMtb at day 3/7/14 Vs day 0 Rx

None applicable

Mtb responses at 7 and 14 daysduring chemotherapy were most similar to that of bacillibefore drug therapy had begun

methylcitrate

[92]

Day14 Vs day2

None applicable

tgs, and ATP-binding cassette transporter and toxin. Rv1258c, bacA, and mmr, rpoB. TA modules, sigma factors

ESX and ribosomal genes, drug-activating enzymes katG, pncA, and ethA, gyrase, bedaquiline target atpE

[94]

BAL vs sputum

7H9/ DTAc

dosR regulon expression was higher in BAL than in sputum

BAL had lower expression of ribosome proteins

[93]

Lipid-NRP1 Vs Dextrose-NRP1

Dubos brothb

Higher virulence, detoxification & adaptation, lipid metabolism, intermediary metabolism& respiration, regulatory protein

Insertion sequences & phages

[60]

In NRP-2 state

7H9/ DTAc

dosR regulon, oxidative stress responses, anaerobic respiration

Growth and metabolism

[93]

  1. The list of genes up /down regulated is not exhaustive, only common genes listed
  2. a7H10 agar with oleic acid-albumin-dextrose-catalase supplement or in 7H9 broth with albumin-dextrose-catalase supplement, 0.2% glycerol and 0.05% Tween-80. Hypoxic (non-replicating persistence) cultures M. tuberculosis strains H37Rv and CH were grown in Dubos Tween albumin broth. bDubos broth (Difco), without glycerol, containing 0.5% albumin, supplemented with either 0.2% dextrose or a lipid mixture (oleic acid, palmitic acid, stearic acid, at final concentration of 0.001% each, plus 0.01% cholesterol). c7H9 media (0.05% Tween 80, 0.2% glycerol, 10% ADC supplement)/ DTA: Dubos Tween albumin; for the NRP-2 model was grown in 100 mL Dubos Tween albumin (DTA). SMtb Sputum Mtb, Mtb Mycobacterium tuberculosis, URG Up regulated genes, DRG Down regulated genes, BAL Broncho alveolar lavage, NRP None replicating persistent state, Vs versus, Rx treatment, dosR Dormancy survival regulator, hspX a-crystallin homologue, narK2 nitrate/ nitrite transporter, qcrC cytochrome bc1 complex, ctaD aa3-type cytochrome c oxidase, icl1 isocitrate lyase gene, nuoB type-I NADH dehydrogenase, Pks12 Polyketide synthase, PDIMs Phthiocerol dimycocerosates, PGLs phenolic glycolipids