Iron deprivation enhances transcriptional responses to in vitro growth arrest of Mycobacterium tuberculosis

Usnic acid impacts energy production and iron metabolism in Mycobacterium tuberculosis H37Rv

Mycobacterium tuberculosis has developed a wide array of response mechanisms to various stress factors. Usnic acid has been demonstrated to be a potent antimycobacterial agent that induces stress responses and growth inhibition in many mycobacterial species. Previous studies have shown that it alters the expression of stress-responsive sigma factors, as well as the metabolites and lipid profile in M. tuberculosis H37Ra. This study was designed to examine potential differences in the strain-specific susceptibility of the virulent H37Rv strain to usnic acid. By combining lipidomic and transcriptomic analyses, we uncovered the impact of usnic acid on bacterial metabolism. The observed downregulation of key lipid classes suggested reduced metabolic activity. The simultaneous elevation of mycobactins-siderophores used by members of the genus Mycobacterium to transport free extracellular iron ions into the cytoplasm-indicated the involvement of iron in the stress response generated by usnic acid. The repressed tricarboxylic acid (TCA) cycle and oxidative phosphorylation were compensated by the upregulation of alternative energy production pathways, such as cytochrome P450 and the ferredoxin reductase system. This indicates that mycobacteria may switch to alternative electron transport mechanisms under usnic acid stress using iron-sulfur clusters to generate energy. From a therapeutic perspective, the study highlights iron metabolism as an essential drug target in mycobacteria. Simultaneously, the results confirm the strain-specific metabolic response of sister strains against the same stressing agent.

IMPORTANCE

A previous study on the influence of usnic acid on the avirulent H37Ra strain revealed that the early bacterial response was associated with redox homeostasis, lipid synthesis, and nucleic acid repair. The response of bacteria to antimicrobials is specific to each species and strain. Given the genetic and phenotypic differences between the avirulent H37Ra strain and the virulent H37Rv strain, we combined lipidomics and global transcriptomics to uncover the mechanism of action of usnic acid against H37Rv. The study identified strain-specific differences between the virulent H37Rv and avirulent H37Ra. The H37Ra strain exhibited increased metabolic activity, while the H37Rv strain showed a reduction in basic metabolic processes and activated alternative iron-dependent energy production. These differences highlight the varying susceptibility of sister strains within the same species to the same antibacterial agent.

Analysis of stress response in multiple bacterial pathogens using a network biology approach

Stress response in bacterial pathogens promotes adaptation, virulence and antibiotic resistance. In this study, a network approach is applied to identify the common central mediators of stress response in five emerging opportunistic pathogens; Enterococcus faecium Aus0004, Staphylococcus aureus subsp. aureus USA300, Klebsiella pneumoniae MGH 78,578, Pseudomonas aeruginosa PAO1, and Mycobacterium tuberculosis H37Rv. A Protein-protein interaction network (PPIN) was constructed for each stressor using Cytoscape3.7.1 from the differentially expressed genes obtained from Gene expression omnibus datasets. A merged PPIN was constructed for each bacterium. Hub-bottlenecks in each network were the central stress response proteins and common pathways enriched in stress response were identified using KOBAS3.0. 31 hub-bottlenecks were common to each individual stress response, merged networks in all five pathogens and an independent cross stress (CS) response dataset of Escherichia coli. The 31 central nodes are in the RpoS mediated general stress regulon and also regulated by other stress response systems. Analysis of the 20 common metabolic pathways modulating stress response in all five bacteria showed that carbon metabolism pathway had the highest crosstalk with other pathways like amino acid biosynthesis and purine metabolism pathways. The central proteins identified can serve as targets for novel wide-spectrum antibiotics to overcome multidrug resistance.

Novel target and cofactor repertoire for the transcriptional regulator JTY_0672 from Mycobacterium bovis BCG

Mycobacterium tuberculosis (Mtb) is the pathogenic agent of tuberculosis (TB). Intracellular survival plays a central role in the pathogenesis of Mtb in a manner that is dependent on an array of transcriptional regulators for Mtb. However, the functionality of JTY_0672, a member of the TetR family of transcriptional regulators, remains unknown. In this study, EMSA, BIL, ChlP-PCR and animal models were used to investigate the regulation function of this protein. We found that the transcriptional regulator JTY_0672 is a broad-spectrum transcriptional regulatory protein and can directly regulate JTY_3148, both in vitro and in vivo. Cofactors containing V B1, V B3, V B6, V C , His, Cys, Asp, Glu, Fe3+, Pb2+, Cu2+, and Li+ were found to inhibit binding between JTY_0672 and the promoter of JTY_3148. JTY_0672 enhanced TAG production and increased Isoniazid (INH) resistance. Besides, this protein either promoted recalcitrance to the host immune response and induced pathological injury and inflammation. In summary, this research identified new targets and cofactors of JTY_0672 and deciphered the physiological functionality of JTY_0672. Our findings will provide an important theoretical basis for understanding the Mtb transcriptional regulatory mechanism.

Prominent transcriptomic changes in Mycobacterium intracellulare under acidic and oxidative stress

BACKGROUND

Mycobacterium avium complex (MAC), including Mycobacterium intracellulare is a member of slow-growing mycobacteria and contributes to a substantial proportion of nontuberculous mycobacterial lung disease in humans affecting immunocompromised and elderly populations. Adaptation of pathogens in hostile environments is crucial in establishing infection and persistence within the host. However, the sophisticated cellular and molecular mechanisms of stress response in M. intracellulare still need to be fully explored. We aimed to elucidate the transcriptional response of M. intracellulare under acidic and oxidative stress conditions.

RESULTS

At the transcriptome level, 80 genes were shown [FC] ≥ 2.0 and p < 0.05 under oxidative stress with 10 mM hydrogen peroxide. Specifically, 77 genes were upregulated, while 3 genes were downregulated. In functional analysis, oxidative stress conditions activate DNA replication, nucleotide excision repair, mismatch repair, homologous recombination, and tuberculosis pathways. Additionally, our results demonstrate that DNA replication and repair system genes, such as dnaB, dinG, urvB, uvrD2, and recA, are indispensable for resistance to oxidative stress. On the contrary, 878 genes were shown [FC] ≥ 2.0 and p < 0.05 under acidic stress with pH 4.5. Among these genes, 339 were upregulated, while 539 were downregulated. Functional analysis highlighted nitrogen and sulfur metabolism pathways as the primary responses to acidic stress. Our findings provide evidence of the critical role played by nitrogen and sulfur metabolism genes in the response to acidic stress, including narGHIJ, nirBD, narU, narK3, cysND, cysC, cysH, ferredoxin 1 and 2, and formate dehydrogenase.

CONCLUSION

Our results suggest the activation of several pathways potentially critical for the survival of M. intracellulare under a hostile microenvironment within the host. This study indicates the importance of stress responses in M. intracellulare infection and identifies promising therapeutic targets.

Tools to develop antibiotic combinations that target drug tolerance in Mycobacterium tuberculosis

Combination therapy is necessary to treat tuberculosis to decrease the rate of disease relapse and prevent the acquisition of drug resistance, and shorter regimens are urgently needed. The adaptation of Mycobacterium tuberculosis to various lesion microenvironments in infection induces various states of slow replication and non-replication and subsequent antibiotic tolerance. This non-heritable tolerance to treatment necessitates lengthy combination therapy. Therefore, it is critical to develop combination therapies that specifically target the different types of drug-tolerant cells in infection. As new tools to study drug combinations earlier in the drug development pipeline are being actively developed, we must consider how to best model the drug-tolerant cells to use these tools to design the best antibiotic combinations that target those cells and shorten tuberculosis therapy. In this review, we discuss the factors underlying types of drug tolerance, how combination therapy targets these populations of bacteria, and how drug tolerance is currently modeled for the development of tuberculosis multidrug therapy. We highlight areas for future studies to develop new tools that better model drug tolerance in tuberculosis infection specifically for combination therapy testing to bring the best drug regimens forward to the clinic.