Analysis of differentially expressed proteins in late-stationary growth phase of Mycobacterium tuberculosis H37Rv

The profile of genome-wide DNA methylation, transcriptome, and proteome in streptomycin-resistant Mycobacterium tuberculosis

Streptomycin-resistant (SM-resistant) Mycobacterium tuberculosis (M. tuberculosis) is a major concern in tuberculosis (TB) treatment. However, the mechanisms underlying streptomycin resistance remain unclear. This study primarily aimed to perform preliminary screening of genes associated with streptomycin resistance through conjoint analysis of multiple genomics. Genome-wide methylation, transcriptome, and proteome analyses were used to elucidate the associations between specific genes and streptomycin resistance in M. tuberculosis H37Rv. Methylation analysis revealed that 188 genes were differentially methylated between the SM-resistant and normal groups, with 89 and 99 genes being hypermethylated and hypomethylated, respectively. Furthermore, functional analysis revealed that these 188 differentially methylated genes were enriched in 74 pathways, with most of them being enriched in metabolic pathways. Transcriptome analysis revealed that 516 genes were differentially expressed between the drug-resistant and normal groups, with 263 and 253 genes being significantly upregulated and downregulated, respectively. KEGG analysis indicated that these 516 genes were enriched in 79 pathways, with most of them being enriched in histidine metabolism. The methylation level was negatively related to mRNA abundance. Proteome analysis revealed 56 differentially expressed proteins, including 14 upregulated and 42 downregulated proteins. Moreover, three hub genes (coaE, fadE5, and mprA) were obtained using synthetic analysis. The findings of this study suggest that an integrated DNA methylation, transcriptome, and proteome analysis can provide important resources for epigenetic studies in SM-resistant M. tuberculosis H37Rv.

Designing New Magic Bullets to Penetrate the Mycobacterial Shield: An Arduous Quest for Promising Therapeutic Candidates

Mycobacterium spp. intimidated mankind since time immemorial. The triumph over this organism was anticipated with the introduction of potent antimicrobials in the mid-20th century. However, the emergence of drug resistance in mycobacteria, Mycobacterium tuberculosis, in particular, caused great concern for the treatment. With the enemy growing stronger, there is an immediate need to equip the therapeutic arsenal with novel and potent chemotherapeutic agents. The task seems intricating as our understanding of the dynamic nature of the mycobacteria requires intense experimentation and research. Targeting the mycobacterial cell envelope appears promising, but its versatility allows it to escape the lethal effect of the molecules acting on it. The unique ability of hiding (inactivity during latency) also assists the bacterium to survive in a drug-rich environment. The drug delivery systems also require upgradation to allow better bioavailability and tolerance in patients. Although the resistance to the novel drugs is inevitable, our commitment to the research in this area will ensure the discovery of effective weapons against this formidable opponent.

Hypobiosis of Mycobacteria: Biochemical Aspects

Under suboptimal growth conditions, bacteria can transit to the dormant forms characterized by a significantly reduced metabolic activity, resistance to various stress factors, and absence of cell proliferation. Traditionally, the dormant state is associated with the formation of highly differentiated cysts and spores. However, non-spore-forming bacteria can transfer to the dormant-like hypobiotic state with the generation of less differentiated cyst-like forms (which are different from spores). This review focuses on morphological and biochemical changes occurred during formation of dormant forms of mycobacteria in particular pathogenic M. tuberculosis (Mtb) caused latent forms of tuberculosis. These forms are characterized by the low metabolic activity, the absence of cell division, resistance to some antibiotics, marked morphological changes, and loss of ability to grow on standard solid media ("non-culturable" state). Being produced in vitro, dormant Mtb retained ability to maintain latent infection in mice. After a long period of dormancy, mycobacteria retain a number of stable proteins with a potential enzymatic activity which could participate in maintaining of low-level metabolic activity in period of dormancy. Indeed, the metabolomic analysis showed significant levels of metabolites in the dormant cells even after a long period of dormancy, which may be indicative of residual metabolism in dormant mycobacteria. Special role may play intracellularly accumulated trehalose in dormant mycobacteria. Trehalose appears to stabilize dormant cells, as evidenced by the direct correlation between the trehalose content and cell viability during the long-term dormancy. In addition, trehalose can be considered as a reserve energy substrate consumed during reactivation of dormant mycobacteria due to the ATP-dependent conversion of trehalase from the latent to the active state. Another feature of dormant mycobacteria is a high representation of proteins participating in the enzymatic defense against stress factors and of low-molecular-weight compounds protecting cells in the absence of replication. Dormant mycobacteria contain a large number of hydrolyzing enzymes, which, on the one hand, ensure inactivation of biomolecules damaged by stress. On the other hand, the products of these enzymatic reactions can be used for the maintenance of energy state and vital activity of bacterial cells during their long-term survival in the dormant state, i.e., for creating a situation that we propose to refer to as the "catabolic survival". In general, dormant non-replicating mycobacterial cells can be described as morphologically altered forms that contain principal macromolecules and are stabilized and protected from the damaging factors by an arsenal of proteins and low-molecular-weight compounds. Because of the presumable occurrence of metabolic reactions in such cells, this form of survival should be referred to as hypobiosis.

Proteomic Analysis of Differentially Expressed Proteins in Mycobacterium Tuberculosis-Infected Macrophages

Background:

Mycobacterium tuberculosis (MTB) and Mycobacterium avium (MA) are intracellular parasitic bacteria. The biological characteristics of MA and MTB are very similar and need to be identified.

Objective:

The study aims to better understand how MTB survives in macrophages and the different pathogenic mechanisms of MTB and MA.

Methods:

The Tandem Mass Tag (TMT) and liquid chromatography-tandem mass spectrometry (LCMS/ MS) were used for analysis of the differentially expressed proteins in MTB-infected macrophages and MA-infected macrophages.

Results:

A total of 682 proteins were found to be differentially expressed in MTB-infected cells in comparison with MA-infected cells. Among these, 10 proteins (O60812, P06576, O43660-2, E9PL10, O00442, M0R050, Q9H8H0, Q9BSJ8, P41240 and Q8TD57-3) were down-regulated in MTB-infected cells, and M0R050, O00442, Q9H8H0, O60812 and O43660 are interactive proteins which participate in a multitude of cellular RNA processing.

Conclusion:

The five down-regulated proteins (M0R050, O00442, Q9H8H0, O60812 and O43660) might repress the synthesis of some resistant proteins in MTB-infected cells to promote MTB survival in macrophages.

Protein Composition of Mycobacterium smegmatis Differs Significantly Between Active Cells and Dormant Cells With Ovoid Morphology

Mycobacteria are able to form dormant cells, which survive for a long time without multiplication. The molecular mechanisms behind prolonged survival of dormant cells are not fully described. In particular, little information is known on biochemical processes which might take place in cells under dormancy. To gain insight into this problem, Mycobacterium smegmatis cells in deep dormant state were obtained after gradual acidification of the growth medium in prolonged stationary phase followed by 1 month of storage at room temperature. Such cells were characterized by low metabolic activity, including respiration, resistance to antibiotics, and altered morphology. The protein composition of cytoplasm and membrane fractions obtained from active and dormant cells were compared by 2D electrophoresis. Almost half of the proteins found in the proteome of dormant cells were absent in that of active cells. This result differs significantly from published results obtained in other studies employing different models of mycobacterium dormancy. This discrepancy could be explained by a deeper dormancy developed in the present model. A feature of a “dormant proteome” is high representation of enzymes involved in glycolysis and defense systems that inactivate or detoxify reactive oxygen and nitrogen species, aldehydes, and oxidized lipids. Dormant mycobacteria are enriched by degradative enzymes, which could eliminate damaged molecules, or the products of such degradation could be reutilized by the cell during prolonged storage. We suggest that some enzymes in dormant cells are inactive, having been used upon transition to the dormant state, or proteins stored in dormant cells for further cell reactivation. At the same time, some proteins could be functional and play roles in maintenance of cell metabolism, albeit at a very slow rate. This study provides a clue as to which biochemical processes could be active under dormancy to ensure long-term viability of dormant mycobacteria.

Proteomics Analysis of Three Different Strains of Mycobacterium tuberculosis under In vitro Hypoxia and Evaluation of Hypoxia Associated Antigen's Specific Memory T Cells in Healthy Household Contacts

In vitro mimicking conditions are thought to reflect the environment experienced by Mycobacterium tuberculosis inside the host granuloma. The majority of in vitro dormancy experimental models use laboratory-adapted strains H37Rv or Erdman instead of prevalent clinical strains involved during disease outbreaks. Thus, we included the most prevalent clinical strains (S7 and S10) of M. tuberculosis from south India in addition to H37Rv for our in vitro oxygen depletion (hypoxia) experimental model. Cytosolic proteins were prepared from hypoxic cultures, resolved by two-dimensional electrophoresis and protein spots were characterized by mass spectrometry. In total, 49 spots were characterized as over-expressed or newly emergent between the three strains. Two antigens (ESAT-6, Lpd) out of the 49 characterized spots were readily available in recombinant form in our lab. Hence, these two genes were overexpressed, purified and used for in vitro stimulation of whole blood collected from healthy household contacts (HHC) and active pulmonary tuberculosis patients (PTB). Multicolor flow cytometry analysis showed high levels of antigen specific CD4(+) central memory T cells in the circulation of HHC compared to PTB (p < 0.005 for ESAT-6 and p < 0.0005 for Lpd). This shows proteins that are predicted to be up regulated during in vitro hypoxia in most prevalent clinical strains would indicate possible potential immunogens. In vitro hypoxia experiments with most prevalent clinical strains would also elucidate the probable true representative antigens involved in adaptive mechanisms.

Comparative Proteomic Analyses of Avirulent, Virulent, and Clinical Strains of Mycobacterium tuberculosis Identify Strain-specific Patterns

Mycobacterium tuberculosis is an adaptable intracellular pathogen, existing in both dormant as well as active disease-causing states. Here, we report systematic proteomic analyses of four strains, H37Ra, H37Rv, and clinical isolates BND and JAL, to determine the differences in protein expression patterns that contribute to their virulence and drug resistance. Resolution of lysates of the four strains by liquid chromatography, coupled to mass spectrometry analysis, identified a total of 2161 protein groups covering ∼54% of the predicted M. tuberculosis proteome. Label-free quantification analysis of the data revealed 257 differentially expressed protein groups. The differentially expressed protein groups could be classified into seven K-means cluster bins, which broadly delineated strain-specific variations. Analysis of the data for possible mechanisms responsible for drug resistance phenotype of JAL suggested that it could be due to a combination of overexpression of proteins implicated in drug resistance and the other factors. Expression pattern analyses of transcription factors and their downstream targets demonstrated substantial differential modulation in JAL, suggesting a complex regulatory mechanism. Results showed distinct variations in the protein expression patterns of Esx and mce1 operon proteins in JAL and BND strains, respectively. Abrogating higher levels of ESAT6, an important Esx protein known to be critical for virulence, in the JAL strain diminished its virulence, although it had marginal impact on the other strains. Taken together, this study reveals that strain-specific variations in protein expression patterns have a meaningful impact on the biology of the pathogen.