1Present address: Nextec Lifesciences, 2/79 Vijay Khand, Gomtinagar, Lucknow 226010, India
Keywords: Mycobacterium bovis BCG; Proteins; Latent state of tuberculosis; Anaerobic non replicating; 2-D gel electrophoresis; Mass spectrometry;
Following initial infection mycobacteria replicate inside host macrophages until an effective immune response is mounted and the bacilli become restricted to the characteristic tuberculous lesions. The bacilli apparently cannot multiply because of oxygen deprivation and other factors [12]. Thus, granuloma is presumed to be the hypoxic environment which is responsible for holding bacterial replication in check and within this anaerobic environment of the caseous necrotic material, the mycobacterial dormancy probably establishes [63]. The ability of M. tuberculosis to persist in the human host may perhaps be due to adaptation to low oxygen environment and obligately aerobic tubercle bacilli are capable of adapting to survive hypoxia by developing into a non replicating or dormant form which maintain viability for extended periods [60, 47]. Furthermore, bacilli in the dormant form are resistant to anti-mycobacterial, thus dormancy might play a role in the persistence of tuberculosis infection despite prolonged chemotherapy.
The ability of M. tuberculosis to persist in a host is a complex process involving the coordinated expression of mycobacterial genes and metabolic pathways to maintain a persistent infection in an immunocompetent host. Defining these factors and their role in bacterial metabolism and physiology, will lead to understanding of biology of latency, drug targets and development of new drugs.
Lack of information about the state of the bacilli during latency hinders our ability to model latent tuberculosis in laboratory settings. However, both in vitro and in vivo systems have been developed which contribute to our current understanding of latency [3, 41, 42, 46 61]. It was shown that in vitro oxygen depletion triggered a dormancy response with a metabolic downshift allowing survival of the bacilli with minimum metabolic activity and oxygen starved bacilli were sensitive to drug metronidazole [60, 61, 64]. Based on these observations investigators have used hypoxic culture condition to generate non replicating persistent mycobacterium as an in vitro surrogate of the metabolic state of the latent TB in vivo, and anaerobic and starved cultures are used as models to study the molecular basis of dormancy [11, 14, 29, 49, 61, 69]. Several attempts were made to examine the protein level response of M. tuberculosis in vitro model systems [37, 43, 57]. The elevated expression of Rv2031c, Rv 3133c, Rv2623 and Rv2626c have been reported during dormant state [5, 11, 68, 69,]. The genetic factors responsible for dormancy are still lesser known.
It has been reported that M. tuberculosis and its close relative M. bovis BCG adapt and survive anaerobiosis by switching from growth to a state of non replicating persistence or dormancy [38, 60, 61,]. Thus, in the present study M. bovis BCG was selected for understanding the adaptive behaviour of mycobacteria to oxygen deprivation conditions. Recombinant M. bovis BCG expressing firefly luciferase was constructed and the condition of non replicating persistent state was standardized. To analyse adaptive mechanisms initiated by M. bovis BCG in response to oxygen depletion, we have used two-dimensional (2-D) gel electrophoresis based protein profiling, which allowed highresolution separation of several hundred proteins, as visualized by Coomassie or silver staining, with both MALDI and tandem electrospray MS. We have been able to identify 34 BCG proteins, the expressions of 28 proteins were either unique or up-regulated and 6 proteins were down regulated during condition of non replicating persistence.
To obtain anaerobic non replicating cultures in dormant state, recombinant BCG, was grown in Fermenter in which the culture self generated a gradual temporal oxygen gradient. With slow depletion of oxygen the culture of BCG was able to adapt and survive anaerobiosis by shifting to a state of non replicating persistence in 22 days which was characterized by stationary CFU at about 6 x 107 cells/ml, 0.4 absorbance at 600 nm, base level RLU, pH drop to 6.4 from 7.2 and < 1% level of dissolved oxygen in the Fermenter (Figure1A-E). Thus, it was observed that with the slow depletion of oxygen recombinant BCG was able to shift to a state of non replicating persistence. Drug susceptibility of recombinant BCG against antimycobacterial compounds in replicating and non replicating states was determined to validate the respective culture conditions because it is known that aerobic replicating mycobacteria are sensitive to killing by rifampicin and not to metronidazole whereas the reverse is true for non replicating persistent bacilli. Non replicating anoxic cultures were found sensitive to killing by metronidazole (99.7% at 120 μ ml-1and 99.87% at 150 mg ml-1) whereas 2% (120 μg ml-1) and 4% (150 mg ml-1) killing was observed for aerobic replicating cells (Figure 2A). On the other hand, rifampicin was found effective against actively replicating (aerobic) cells and non replicating anoxic cells were resistant to killing by rifampicin (Figure 2B).
Protein name / |
Spot |
SWISS-PROT |
Mass/PI |
Function |
MALDI- MS |
No. of |
Sequence |
Rv0148 |
15 |
P96825 |
29.8/5.12 |
Oxidoreductase |
69 |
2 |
57.0 |
Rv0183 |
24 |
Q7DAB5
|
30.3/6.18 |
Possible lysophospholipase |
128 |
2 |
46 |
FabG4/Rv0242c |
5, 27 |
O53665
|
46.7/6.38
|
Probable 3-oxoacyl- |
69 |
7 |
25.1 |
FadE5/Rv0244c |
9 |
O53666
|
66.0/5.19 |
Probable acyl-coA dehydrogenase |
135 |
18 |
47.5 |
Acr2/Rv0251c |
28 |
O53673 |
17.7/5.04 |
Heat shock protein |
86 |
6 |
65.3 |
DnaK/Rv0350 |
7 |
P32723
|
66.8/4.59 |
Probable chaperone, |
231 |
4 |
66.0 |
GroEL/Rv0440 |
4,8,20 |
P06806 |
56.5/4.5 |
60 kDa chaperonin 2 |
63 |
5 |
37.0 |
Tuf/Rv0685 |
13 |
P31501 |
43.5/5.12 |
Probable iron-regulated elongation factor |
81 |
15 |
46.2 |
PurC/Rv0780 |
6 |
Q59566
|
32.9/4.95 |
Phosphoribosylaminoimidazole- succinocarboxamide synthase |
64 |
8 |
37.0 |
FadB/Rv0860 |
12 |
Q7D952 |
76.1/5.21 |
Probable fatty oxidation protein |
81 |
13 |
20.4 |
TrpC/Rv1611 |
25 |
O06129
|
28.1/4.86 |
Probable indole-3-glycerol phosphate synthase |
80 |
9 |
38.2 |
TB16.3/Rv2185c |
19 |
O53519 |
16.3/4.48 |
Conserved hypothetical protein |
70 |
9 |
59 |
SucB/Rv2215 |
10,11 |
Q10381 |
57.1/4.64 |
Probable pyruvate dehydrogenase |
90 |
12 |
28.4 |
AccD6/Rv2247 |
26 |
Q10506 |
56.5/5.0 |
Acetyl/propionyl-coA carboxylase |
98 |
11 |
23.1 |
NdkA/Rv2445c |
1 |
P71904 |
14.5/5.18 |
Probable nucleoside diphosphate kinase |
65 |
6 |
53.7 |
ClpP1/Rv2461c |
18 |
O53188 |
21.6/4.54 |
Probable ATP-dependent |
151 |
2 |
81.0 |
Rv2626c |
3 |
O06186 |
15.6/4.8 |
Conserved hypothetical protein |
65 |
7 |
62.9 |
Mpt70/Rv2875 |
23 |
Q50769 |
19.1/4.54 |
Major secreted immunogenic protein |
109 |
7 |
67.3 |
GroES/Rv3418c |
2,16,17 |
P09621 |
10.7/4.5 |
Heat shock protein, chaperonin |
67 |
6 |
42.4 |
IlvX/Rv3509c |
21 |
G70806
|
52.1/4.53
|
Probable |
71 |
12 |
26.8 |
Ppa/Rv3628 |
22 |
O06379 |
18.3/4.52 |
Inorganic pyrophosphatase |
62 |
7 |
45.7 |
BfrB/Rv3841 |
14 |
F70653 |
20.4/4.23 |
Bacterioferritin |
77 |
2 |
62 |
Protein name/ |
Spot |
SWISS-PROT |
Mass/PI |
Function |
MALDI- MS Score |
No. of |
Sequence |
Icl/Rv0467 |
32 |
O53752 |
47.1/4.79 |
Isocitrate lyase |
89 |
15 |
53.7 |
GreA/Rv1080c |
33 |
O53428 |
17.8/4.63 |
Probable transcription elongation factor |
104 |
10 |
73.8 |
AhpE/Rv2238c |
29 |
Q10520 |
16.8/5.12 |
Probable |
72 |
2 |
54. |
KasA/Rv2245 |
31 |
Q10524 |
43.3/4.93 |
3-oxoacyl-synthase |
78 |
10 |
39.4 |
Tsf/Rv2889c
|
30 |
Q10788 |
28.7/5.01 |
Probable elongation factor |
82 |
10 |
44.6 |
LeuC/Rv2988c |
34 |
O53237 |
50.2/5.29 |
Probable 3-isopropylmalate dehydratase |
78 |
15 |
37.8 |
During stress conditions the low metabolic activity of mycobacteria most probably leads to reduced RNA and protein synthesis. In our study, EF-TS, Probable elongation factor and GreA, a probable transcription elongation factor necessary for efficient RNA polymerase transcription elongation past templateencoded arresting sites, were found to be down regulated.
Rv0148 codes for NADP dependent dehydrogenases, the short-chain alcohol dehydrogenase superfamily. Members of this subgroup are known to act on a large variety of substrates, including sugars, steroids, aromatic hydrocarbons, antibiotics, and compounds involved in nitrogen metabolism. In contrast to our results, it was downregulated in low-iron-concentration medium [66]. We observed induction of PurC, involved in de novo purine biosynthesis and TrpC (Rv1611) which is a probable indole-3-glycerol phosphate synthase involved in tryptophan biosynthesis [30]. TrpC was also upregulated in M. tuberculosis during oxygen depletion [9]. Ppa encoding inorganic pyrophosphatase, plays an important role in macromolecular biosynthesis and is considered essential for the viability of E. coli and yeast and induced during intracellular infection of Legionella pneumophila in U937 macrophage-like cells [8, 35, 39]. ilvX codes for a probable acetolactate synthase that catalyzes a reversible reaction to form pyruvate from acetolactate, and could be involved in valine and isoleucine biosynthesis. These are essential amino acids that are not available to mycobacteria during growth in host and the auxotrophic strain of mycobacteria could not proliferate in eukaryotic tissues thus could be a target for new drug development [24, 25].
ClpP proteases are known to degrade proteins that cannot be refolded in gram-positive bacteria and expressed in response to stress and required for survival [18, 19, 21, 22, 34, 36, 48]. Experiments revealed that ClpP is important for S. typhimurium to grow under various stressful conditions, such as low pH, elevated temperature and high salt concentrations [58]. BfrB, a bacterioferritin, involved in intracellular storage of iron and induced under at reduced oxygen atmosphere and elevated temperatures [53, 56]. Induction of iron storage gene during anaerobic persistence may be required to increase iron stores for use during long periods of dormancy. LeuC, involved in leucine biosynthesis, was down-regulated after nutrient starvation as observed in our study in response to hypoxia The role of LeuC in relation to oxidative stress has not been elucidated but leucine auxotrophy is known to restrict the growth of M. bovis BCG in the macrophages [2, 3].
ICL, isocitrate lyase is one of the first M. tuberculosis proteins shown to be required for persistent infection an initial enzyme in the glyoxylate shunt, allows bacteria to utilize fatty acids as carbon sources when the availability of primary carbon sources is limiting [44]. Expression of ICL in human lung granulomas in cultured macrophages and in microaerophilic conditions has been reported [16, 23, 62, 49]. But in our study, the downregulation of ICL appears to match the reported decrease in transcription and expression of the enzyme during hypoxia in M. bovis BCG [28, 38].
The downregulation of AhpE encoding probable peroxiredoxin, involved in detoxification of organic peroxides suggesting that this protein may not required during hypoxia [6, 7].
In conclusion, therefore, the differential protein expression described herein during non replicating persistence of M. bovis BCG involved in stress responses and metabolic pathways may suggest that the expression of preferred proteins is essential for survival. The non-replicating persistence phenotype of is assumed to be responsible for the maintenance of latent infection and the requirement of a long treatment duration for active tuberculosis. A better understanding of mycobacterial gene expression under anaerobic non replicating conditions may provide insight in to the mechanism of adaptation of mycobacteria inside the host and may represent biomarkers for identification and development of new drug targets. It is interesting that some of the proteins identified in our study have also been reported earlier with M. tuberculosis [3, 49, 53, 55]. To further enhance understanding of latent M. tuberculosis as well as BCG, the role of the identified proteins in response to hypoxia must be elucidated. 6.
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