@article {164006, title = {The lipid language of tuberculosis: surface molecules in host interaction and drug resistance.}, journal = {mBio}, year = {2026}, month = {2026 Feb 02}, pages = {e0395925}, abstract = {

(), the causative agent of tuberculosis (TB), is a uniquely successful pathogen due in large part to its complex lipid-rich cell envelope. Comprising nearly 40\% of its dry weight, lipids-such as mycolic acids, phthiocerol dimycocerosates (PDIM), trehalose dimycolate (TDM), and sulfolipids (SLs)-play crucial roles in infection, immune evasion, intracellular persistence, granuloma formation, transmission, and drug resistance. These lipids modulate host-pathogen interactions by altering host membrane biophysics, hijacking phagosome maturation, and interfering with host immune pathways, including autophagy and inflammatory signaling. Upon inhalation, surface lipids inhibit pulmonary surfactant function and mask pathogen-associated molecular patterns, facilitating uptake by permissive macrophage subsets. Intracellularly, lipoglycans like mannose-capped lipoarabinomannan block phagolysosome fusion, while PDIM and TDM promote phagosomal escape and subversion of vesicular trafficking. Lipid-mediated modulation of autophagy pathways further enhances bacterial survival within host cells. In addition to shaping host immune responses, lipids orchestrate granuloma development and promote pathological features such as foam cell formation and caseation, which are central to transmission. Specifically, phenolic glycolipids and SLs stimulate neuronal pathways, triggering cough, thereby facilitating aerosol spread. Finally, the lipid-rich envelope acts as a formidable barrier to antibiotics, with resistance partly driven by the altered lipid composition and architecture in multidrug-resistant strains. Targeting lipid biosynthesis and transport pathways offers promising avenues for novel anti-TB therapies. This review highlights the multifaceted roles of lipids at the host-pathogen interface, recent technical advances enabling these insights, and emerging challenges in translating lipid biology into improved TB control.

}, keywords = {cell wall, Host-Pathogen Interactions, Mtb lipids, multidrug resistance, Mycobacterium tuberculosis, pathogenesis.}, issn = {2150-7511}, doi = {10.1128/mbio.03959-25}, url = {https://pubmed.ncbi.nlm.nih.gov/41627032/}, author = {Radhakrishnan, Sandhya Krishnan and Sundaramurthy, Varadharajan} } @article {161133, title = {Bioenergetic reprogramming of macrophages reduces drug tolerance in Mycobacterium tuberculosis.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Oct 23}, pages = {9370}, abstract = {

Effective clearance of Mycobacterium tuberculosis (Mtb) requires targeting drug-tolerant populations within host macrophages. Here, we show that macrophage metabolic states govern redox heterogeneity and drug response in intracellular Mtb. Using a redox-sensitive fluorescent reporter (Mrx1-roGFP2), flow cytometry, and transcriptomics, we found that macrophages with high oxidative phosphorylation (OXPHOS) and low glycolysis harbor reductive, drug-tolerant Mtb, whereas glycolytically active macrophages generate mitochondrial ROS via reverse electron transport, imposing oxidative stress on Mtb and enhancing drug efficacy. Computational and genetic analyses identified NRF2 as a key regulator linking host metabolism to bacterial redox state and drug tolerance. Pharmacological reprogramming of macrophages with the FDA-approved drug meclizine (MEC) shifted metabolism towards glycolysis, suppressed redox heterogeneity, and reduced Mtb drug tolerance in macrophages and mice. MEC exhibited no adverse interactions with frontline anti-TB drugs. These findings demonstrate the therapeutic potential of host metabolic reprogramming to overcome Mtb drug tolerance.

}, keywords = {Animals, Antitubercular Agents, Drug Tolerance, Energy Metabolism, Female, Glycolysis, Humans, Macrophages, Mice, Mice, Inbred C57BL, Mitochondria, Mycobacterium tuberculosis, NF-E2-Related Factor 2, Oxidation-Reduction, Oxidative Phosphorylation, Oxidative Stress, Reactive Oxygen Species, Tuberculosis}, issn = {2041-1723}, doi = {10.1038/s41467-025-64407-w}, author = {Yadav, Vikas and Sahoo, Sarthak and Malhotra, Nitish and Mishra, Richa and Sreedharan, Sreesa and Rajmani, Raju S and Shanmugam, Siva and Shandil, Radha K and Narayanan, Shridhar and Thacker, Vivek V and Laxman, Sunil and Jolly, Mohit Kumar and Seshasayee, Aswin Sai Narain and Singh, Amit} } @article {153398, title = {Computational analysis of the effect of a binding protein (RbpA) on the dynamics of Mycobacterium tuberculosis RNA polymerase assembly.}, journal = {PLoS One}, volume = {20}, year = {2025}, month = {2025}, pages = {e0317187}, abstract = {

BACKGROUND: RNA polymerase-binding protein A (RbpA) is an actinomycetes-specific protein crucial for the growth and survival of the pathogen Mycobacterium tuberculosis. Its role is essential and influences the transcription and antibiotic responses. However, the regulatory mechanisms underlying RbpA-mediated transcription remain unknown. In this study, we employed various computational techniques to investigate the role of RbpA in the formation and dynamics of the RNA polymerase complex.

RESULTS: Our analysis reveals significant structural rearrangements in RNA polymerase happen upon interaction with RbpA. Hotspot residues, crucial amino acids in the RbpA-mediated transcriptional regulation, were identified through our examination. The study elucidates the dynamic behavior within the complex, providing insights into the flexibility and functional dynamics of the RbpA-RNA polymerase interaction. Notably, potential allosteric mechanisms, involving the interface of subunits α1 and α2 were uncovered, shedding light on how RbpA modulates transcriptional activity.

CONCLUSIONS: Finally, potential ligands meant for the α1-α2 binding site were identified through virtual screening. The outcomes of our computational study serve as a foundation for experimental investigations into inhibitors targeting the RbpA-regulated dynamics in RNA polymerase. Overall, this research contributes valuable information for understanding the intricate regulatory networks of RbpA in the context of transcription and suggests potential avenues for the development of RbpA-targeted therapeutics.

}, keywords = {Bacterial Proteins, Binding Sites, DNA-Directed RNA Polymerases, Molecular Dynamics Simulation, Mycobacterium tuberculosis, Protein Binding, Transcription, Genetic}, issn = {1932-6203}, doi = {10.1371/journal.pone.0317187}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0317187}, author = {Bheemireddy, Sneha and Sowdhamini, Ramanathan and Srinivasan, Narayanaswamy} } @article {157492, title = {M. tuberculosis surface sulfoglycolipid SL-1 activates the mechanosensitive channel TRPV4 to enhance lysosomal biogenesis and exocytosis in macrophages}, journal = {Mol Biol Cell}, volume = {36}, year = {2025}, month = {2025 Jun 01}, pages = {ar76}, abstract = {

Intracellular pathogens manipulate host cellular pathways to ensure their survival. (Mtb) disrupts phagosomal trafficking to prevent fusion with lysosomes. Beyond this localized effect, Mtb globally remodels the host lysosomal system, predominantly through its virulence-associated surface lipid, sulfolipid-1 (SL-1). SL-1 enhances lysosomal biogenesis via the mTORC1-TFEB axis; however, the upstream mediators remain unknown. Here, we show that SL-1 induces calcium influx into macrophages and identify the mechanosensitive calcium channel transient receptor potential vanilloid subtype 4 (TRPV4) as a crucial upstream mediator of SL-1-induced lysosomal remodeling. TRPV4 influences multiple aspects of lysosomal function, including biogenesis, acidification, enzymatic activity, phagosome maturation, and lysosomal exocytosis. These effects are recapitulated during Mtb infection, underscoring the relevance of SL-1- and TRPV4-dependent lysosomal remodeling in an infection context. TRPV4 expression is upregulated during Mtb infection and partially localizes to both lysosomes and the Mtb-containing vacuole. Remarkably, TRPV4 activation, independent of SL-1, is sufficient to enhance lysosomal biogenesis, identifying TRPV4 as a key regulator of lysosomal homeostasis. Together, these findings uncover a novel mechanism of lysosomal remodeling driven by a pathogen lipid virulence factor and reveal a previously unrecognized role for TRPV4 in modulating lysosomal homeostasis in macrophages.

}, keywords = {Animals, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Calcium, Exocytosis, Glycolipids, Humans, Lysosomes, Macrophages, Mice, Mice, Inbred C57BL, Mycobacterium tuberculosis, Phagosomes, TRPV Cation Channels}, issn = {1939-4586}, doi = {10.1091/mbc.E24-12-0560}, url = {https://www.molbiolcell.org/doi/10.1091/mbc.E24-12-0560?url_ver=Z39.88-2003\&rfr_id=ori:rid:crossref.org\&rfr_dat=cr_pub\%20\%200pubmed}, author = {Umar, Ibrahim and Gulzar, Shah-E-Jahan and Sundaramurthy, Varadharajan} } @article {147303, title = {Intracellular peroxynitrite perturbs redox balance, bioenergetics, and Fe-S cluster homeostasis in Mycobacterium tuberculosis.}, journal = {Redox Biol}, volume = {75}, year = {2024}, month = {2024 Sep}, pages = {103285}, abstract = {

The ability of Mycobacterium tuberculosis (Mtb) to tolerate nitric oxide (NO) and superoxide (O) produced by phagocytes contributes to its success as a human pathogen. Recombination of NO and O generates peroxynitrite (ONOO), a potent oxidant produced inside activated macrophages causing lethality in diverse organisms. While the response of Mtb toward NO and O is well established, how Mtb responds to ONOO remains unclear. Filling this knowledge gap is important to understand the persistence mechanisms of Mtb during infection. We synthesized a series of compounds that generate both NO and O, which should combine to produce ONOO. From this library, we identified CJ067 that permeates Mtb to reliably enhance intracellular ONOO levels. CJ067-exposed Mtb strains, including multidrug-resistant (MDR) and extensively drug-resistant (XDR) clinical isolates, exhibited dose-dependent, long-lasting oxidative stress and growth inhibition. In contrast, Mycobacterium smegmatis (Msm), a fast-growing, non-pathogenic mycobacterial species, maintained redox balance and growth in response to intracellular ONOO. RNA-sequencing with Mtb revealed that CJ067 induces antioxidant machinery, sulphur metabolism, metal homeostasis, and a 4Fe-4S cluster repair pathway (suf operon). CJ067 impaired the activity of the 4Fe-4S cluster-containing TCA cycle enzyme, aconitase, and diminished bioenergetics of Mtb. Work with Mtb strains defective in SUF and IscS involved in Fe-S cluster biogenesis pathways showed that both systems cooperatively protect Mtb from intracellular ONOO in vitro and inducible nitric oxide synthase (iNOS)-dependent growth inhibition during macrophage infection. Thus, Mtb is uniquely sensitive to intracellular ONOO and targeting Fe-S cluster homeostasis is expected to promote iNOS-dependent host immunity against tuberculosis (TB).

}, keywords = {Energy Metabolism, Homeostasis, Humans, Iron-Sulfur Proteins, Macrophages, Mycobacterium smegmatis, Mycobacterium tuberculosis, Nitric Oxide, Oxidation-Reduction, Oxidative Stress, Peroxynitrous Acid, Superoxides, Tuberculosis}, issn = {2213-2317}, doi = {10.1016/j.redox.2024.103285}, author = {Dewan, Arshiya and Jain, Charu and Das, Mayashree and Tripathi, Ashutosh and Sharma, Ajay Kumar and Singh, Harshit and Malhotra, Nitish and Seshasayee, Aswin Sai Narain and Chakrapani, Harinath and Singh, Amit} } @article {137347, title = {Cysteine desulfurase (IscS)-mediated fine-tuning of bioenergetics and SUF expression prevents hypervirulence.}, journal = {Sci Adv}, volume = {9}, year = {2023}, month = {2023 Dec 15}, pages = {eadh2858}, abstract = {

Iron-sulfur (Fe-S) biogenesis requires multiprotein assembly systems, SUF and ISC, in most prokaryotes. () encodes a complete SUF system, the depletion of which was bactericidal. The ISC operon is truncated to a single gene (cysteine desulfurase), whose function remains uncertain. Here, we show that Δ is bioenergetically deficient and hypersensitive to oxidative stress, antibiotics, and hypoxia. Δ resisted killing by nitric oxide (NO). RNA sequencing indicates that IscS is important for expressing regulons of DosR and Fe-S-containing transcription factors, WhiB3 and SufR. Unlike wild-type , Δ could not enter a stable persistent state, continued replicating in mice, and showed hypervirulence. The operon was overexpressed in Δ during infection in a NO-dependent manner. Suppressing expression in Δ either by CRISPR interference or upon infection in inducible NO-deficient mice arrests hypervirulence. Together, redesigned the ISC system to "fine-tune" the expression of SUF machinery for establishing persistence without causing detrimental disease in the host.

}, keywords = {Animals, Energy Metabolism, Escherichia coli, Iron-Sulfur Proteins, Mice, Mycobacterium tuberculosis}, issn = {2375-2548}, doi = {10.1126/sciadv.adh2858}, author = {Das, Mayashree and Sreedharan, Sreesa and Shee, Somnath and Malhotra, Nitish and Nandy, Meghna and Banerjee, Ushashi and Kohli, Sakshi and Rajmani, Raju S and Chandra, Nagasuma and Seshasayee, Aswin Sai Narain and Laxman, Sunil and Singh, Amit} } @article {135860, title = {Structural snapshots of Mycobacterium tuberculosis enolase reveal dual mode of 2PG binding and its implication in enzyme catalysis.}, journal = {IUCrJ}, volume = {10}, year = {2023}, month = {2023 Nov 01}, pages = {738-753}, abstract = {

Enolase, a ubiquitous enzyme, catalyzes the reversible conversion of 2-phosphoglycerate (2PG) to phosphoenolpyruvate (PEP) in the glycolytic pathway of organisms of all three domains of life. The underlying mechanism of the 2PG to PEP conversion has been studied in great detail in previous work, however that of the reverse reaction remains to be explored. Here we present structural snapshots of Mycobacterium tuberculosis (Mtb) enolase in apo, PEP-bound and two 2PG-bound forms as it catalyzes the conversion of PEP to 2PG. The two 2PG-bound complex structures differed in the conformation of the bound product (2PG) viz the widely reported canonical conformation and a novel binding pose, which we refer to here as the alternate conformation. Notably, we observed two major differences compared with the forward reaction: the presence of Mg is non-obligatory for the reaction and 2PG assumes an alternate conformation that is likely to facilitate its dissociation from the active site. Molecular dynamics studies and binding free energy calculations further substantiate that the alternate conformation of 2PG causes distortions in both metal ion coordination and hydrogen-bonding interactions, resulting in an increased flexibility of the active-site loops and aiding product release. Taken together, this study presents a probable mechanism involved in PEP to 2PG catalysis that is likely to be mediated by the conformational change of 2PG at the active site.

}, keywords = {Catalysis, Models, Molecular, Mycobacterium tuberculosis, Phosphopyruvate Hydratase, Protein Conformation}, issn = {2052-2525}, doi = {10.1107/S2052252523008485}, author = {Ahmad, Mohammed and Jha, Bhavya and Bose, Sucharita and Tiwari, Satish and Dwivedy, Abhisek and Kar, Deepshikha and Pal, Ravikant and Mariadasse, Richard and Parish, Tanya and Jeyakanthan, Jeyaraman and Vinothkumar, Kutti R and Biswal, Bichitra Kumar} } @article {908, title = {Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function.}, journal = {Tuberculosis (Edinb)}, volume = {95}, year = {2015}, month = {2015 Jan}, pages = {14-25}, abstract = {

The availability of the genome sequence of Mycobacterium tuberculosis H37Rv has encouraged determination of large numbers of protein structures and detailed definition of the biological information encoded therein; yet, the functions of many proteins in M. tuberculosis remain unknown. The emergence of multidrug resistant strains makes it a priority to exploit recent advances in homology recognition and structure prediction to re-analyse its gene products. Here we report the structural and functional characterization of gene products encoded in the M. tuberculosis genome, with the help of sensitive profile-based remote homology search and fold recognition algorithms resulting in an enhanced annotation of the proteome where 95\% of the M. tuberculosis proteins were identified wholly or partly with information on structure or function. New information includes association of 244 proteins with 205 domain families and a separate set of new association of folds to 64 proteins. Extending structural information across uncharacterized protein families represented in the M. tuberculosis proteome, by determining superfamily relationships between families of known and unknown structures, has contributed to an enhancement in the knowledge of structural content. In retrospect, such superfamily relationships have facilitated recognition of probable structure and/or function for several uncharacterized protein families, eventually aiding recognition of probable functions for homologous proteins corresponding to such families. Gene products unique to mycobacteria for which no functions could be identified are 183. Of these 18 were determined to be M. tuberculosis specific. Such pathogen-specific proteins are speculated to harbour virulence factors required for pathogenesis. A re-annotated proteome of M. tuberculosis, with greater completeness of annotated proteins and domain assigned regions, provides a valuable basis for experimental endeavours designed to obtain a better understanding of pathogenesis and to accelerate the process of drug target discovery.

}, keywords = {Hydrolases, Mycobacterium tuberculosis, Protein Structure, Tertiary, Proteome, Sequence Analysis, Protein, Structural Homology, Protein}, issn = {1873-281X}, doi = {10.1016/j.tube.2014.10.009}, author = {Ramakrishnan, Gayatri and Ochoa-Monta{\~n}o, Bernardo and Raghavender, Upadhyayula S and Mudgal, Richa and Joshi, Adwait G and Chandra, Nagasuma R and Sowdhamini, Ramanathan and Blundell, Tom L and Srinivasan, Narayanaswamy} }