Biology subjects

Bamniya, B.

Publications and source records attributed to Bamniya, B..

5 recordsLinked to original sources

bioRxiv2025

Uncovering asparagine utilization pathway, a critical requirement for mycobacterial pH-driven adaptation at the host-pathogen crossroads

M. tuberculosis, an intracellular pathogen, thrives in a specialized membrane-bound vacuole, the phagosome with acidic pH and limited access to nutrients. To survive and replicate within human host, M. tuberculosis must adapt and fulfil its nutritional requirements. To understand how the bacillus captures nutrients from its host, we studied mycobacterial acquisition of host-derived amino acids, the preferred nitrogen sources. We discovered that PhoP, a key determinant of mycobacterial adaptation to phagosomal acidification, controls expression of AnsP1 and AnsP2 to facilitate acquisition of host aspartate and asparagine, respectively. Thus, macrophage-infected WT-H37Rv showed a significantly higher level of intra-bacterial Asn compared to the phoP-KO mutant and a complemented mutant could restore Asn level to that of WT-H37Rv. Under acidic conditions, elevated DNA binding of PhoP within the promoters lead to direct activation of ansP1 and ansP2. Consistently, phoP-KO is unable to utilize Asn under acidic condition, and over-expression of ansP1 or ansP2 restored intracellular growth defect of the mutant. These findings uncover the regulatory network allowing utilization of organic nitrogen sources by the pathogen during infection. Author summaryHuman Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a global public health burden claiming [~]1.25 million deaths in 2023. To investigate how the bacillus captures nitrogen sources from its host, we studied acquisition of host amino acids aspartate (Asp) and asparagine (Asn) by the tubercle bacilli. We show that PhoP, a key determinant of mycobacterial adaptation to phagosomal acidification, controls expression of Asp and Asn transporters to facilitate acquisition of host amino acids by the pathogen. A mutant lacking phoP is unable to utilize Asn under acidic conditions, whereas over-expression of ansP1 and/or ansP2 restored growth defect of the phoP-KO in vitro and in macrophages. Together, these findings uncover the transcriptional landscape allowing utilization of organic nitrogen sources by the tubercle bacilli during infection.

microbiology↗

bioRxiv2025

A repressor co-regulatory network integrates iron acquisition to mycobacterial stress tolerance

Growing evidence suggests that controlled regulation of iron (Fe) uptake is essential for mycobacterial survival and proliferation in the host. In this study, we discovered the mechanism that links mycobacterial Fe acquisition to intra-bacterial redox environment via the phoP locus. Remarkably, regulated expression of the major Fe storage protein encoding gene bfrB determines bacterial tolerance to oxidative stress and intracellular survival of the pathogen. Transcriptomic analysis coupled with in vivo DNA binding studies uncover a distinct IdeR-independent regulation, which utilizes Lsr2 and virulence regulator PhoP to modulate transcriptional control of bfrB via recruitment of both the regulators. A striking inhibition of Lsr2 binding to the bfrB promoter in a phoP-KO mutant, attributable to Lsr2-PhoP protein-protein interaction, provides the most fundamental biological insight. Building on these results, we proposed a model suggesting how Lsr2-PhoP interaction (or lack thereof) contributes to repression and/or stress-specific activation of bfrB expression. Collectively, these results uncover a key mechanism linking Fe acquisition and oxidative stress response of mycobacteria, and have significant implications on the intracellular survival of the pathogen.

microbiology↗

bioRxiv2024

Context-dependent acetylation of the virulence regulator PhoP accounts for carbon-source specific mycobacterial growth inhibition under acidic conditions

Mycobacterium tuberculosis PhoP is essential for intracellular survival and virulence of the tubercle bacilli. Genetic evidences coupled with biochemical studies uncover that PhoP affects various aspects of M. tuberculosis pathophysiology including pH sensing during intracellular adaptation and carbon source utilization. Building on this observation, herein we report essentiality of the phoP locus in carbon-source specific mycobacterial growth. Further, our results on mycobacterial growth in the presence of different carbon sources suggest accumulation of acetyl CoA, a metabolic intermediate which acetylates major transcription factors. To explore the mechanism, we examined in vivo acetylation of PhoP, and our results suggest a link between acetylation of PhoP and mycobacterial carbon source utilization. Using a genetic screening, we identified PhoP-specific mycobacterial acetylases. Our two major findings that (a) acidic conditions of growth inhibit PhoP acetylation, which represses PhoP regulon by interfering with DNA binding activity of the regulator and (b) mycobacteria expressing acetylation-defective PhoP shows growth inhibition, together suggest a role of acetylation on mycobacterial growth via carbon-source utilization. These results have implications on intracellular survival and growth program of mycobacteria under varying environmental cues.

microbiology↗

bioRxiv2023

Dual functioning by the PhoR sensor is a key determinant to Mycobacterium tuberculosis virulence

PhoP-PhoR empowers M. tuberculosis to adapt to diverse environmental conditions, and remains essential for virulence. Although PhoP and PhoR have been structurally characterized, the signal(s) that this TCS responds to remains unknown. In this study, we show that PhoR is a sensor of acidic pH/high salt conditions, which activate PhoP via phosphorylation. Transcriptomic studies uncover that acidic pH-inducible expression of PhoP regulon is significantly inhibited in a PhoR-deleted M. tuberculosis. Using genome-wide screening we further identify a non-canonical mechanism of PhoP phosphorylation by the sensor kinase PrrB. To investigate how phosphorylation of PhoP is regulated, we discovered that PhoR functions as a phosphatase. Our results identify the motif/residues responsible for contrasting kinase/phosphatase dual functioning of PhoP, and collectively determine the homeostatic regulation of intra-mycobacterial P~PhoP which controls the final output of PhoP regulon. Together, these data uncover that PhoR plays a central role in mycobacterial adaptation to low pH conditions within the host macrophage phagosome. Consistent with these results a PhoR-deleted M. tuberculosis remains significantly attenuated in macrophages and animal models.

microbiology↗

bioRxiv2022

Mycobacterial virulence regulator integrates cAMP homeostasis with stress response and virulence

Survival of M. tuberculosis within the host macrophages requires the bacterial virulence regulator PhoP, but the underlying reason remains unknown. cAMP is one of the most widely used second messengers, which impacts on a wide range of cellular responses in microbial pathogens including M. tuberculosis. Herein, we hypothesized that intra-bacterial cAMP level could be controlled by PhoP since this major regulator plays a key role in bacterial responses against numerous stress conditions. A transcriptomic analysis reveals that PhoP functions as a repressor of cAMP-specific phosphodiesterase (PDE) Rv0805, which hydrolyses cAMP. In keeping with these results, we find specific recruitment of the regulator within the promoter region of rv0805 PDE, and absence of phoP or ectopic expression of rv0805 independently accounts for elevated PDE synthesis leading to depletion of intra-bacterial cAMP level. Thus, genetic manipulation to inactivate PhoP-rv0805-cAMP pathway decreases cAMP level, stress tolerance and intracellular survival of the bacillus.

microbiology↗