Biology subjects

Chandra, N.

Publications and source records attributed to Chandra, N..

16 recordsLinked to original sources

bioRxiv2025

CAcnesDB: A database of Cutibacterium acnes with Integrated Functional Insights derived from Multi-modal Genome Annotation

Cutibacterium acnes is a predominant member of the human skin microbiome, generally as a beneficial or a benign inhabitant, which under specific conditions transforms into a pathogen, causing acne and associated inflammatory responses. While there is a wealth of data on the microbiology and genomics of the microbe, there is a lack of comprehensive annotation of the proteins coded by the genome, slowing progress in understanding its unique metabolic versatility and survival in host hypoxic sebaceous niches. We configured an integrated pipeline for functional annotation of the C. acnes genome, combining gene calling, domain and ontology mapping, KEGG pathways assignment, proteome-scale structural modeling, predicting Pockets and associating the small-molecule metabolites based on binding site similarity to facilitate structure-to-function annotation. Structural predictions using ColabFold covered nearly the full proteome, with 67.4% of models showing high confidence. To infer protein function, ligand-binding sites in the C. acnes modeled proteome were predicted using a consensus of three independent algorithms, PocketDepth, SiteHound, and FPocket. The resulting pockets were matched with known small-molecule binding sites in PDB to map potential ligands, resulting in the C. acnes predicted metabolome (CApM) comprising 1,954 ligands across 1,865 proteins. CAcnesDB is a comprehensive up-to-date database of the C. acnes genome, hosting functional annotation from multiple levels of input and analyses, covering 2297 protein-coding genes. Impact StatementCutibacterium acnes (C. acnes) is implicated in acne vulgaris, a common skin condition affecting millions of people worldwide, yet the absence of a unified genomic resource limits comprehensive understanding of the underlying biology. In this work, we introduce CAcnesDB, a genome-wide annotation resource built through multi-modal integration of sequence- and structure-based analyses, structural proteome models, predicted binding sites associated with small-molecule metabolites, functional classes, protein-protein interactions, and pathways. This resource consolidates enriched annotations to enable systematic exploration of C. acnes biology and pathogenic mechanisms. We showcase its utility through detailed analyses of membrane transporters and hypothetical proteins, highlighting novel functional insights into this skin microbe. Given the clinical relevance of C. acnes in skin health and its role in skincare product development, CAcnesDB represents a valuable platform for both basic research and translational applications.

bioinformatics↗

bioRxiv2025

Balance between autophagy and apoptosis determines anoikis resistance: a mathematical model on cell fate

Although several cancer cells are shed into circulation, most die due to stress, including loss of matrix attachment which triggers anoikis. A subset, however, acquires anoikis resistance, and survives to seed metastasis. How matrix-deprived cancer cells balance autophagy and apoptosis to decide cell fate remains unclear. Here, we formulated a deterministic ordinary differential equation (ODE)-based model of Akt-AMPK-ERK signal interaction to study this balance. Simulations revealed that high AMPK activity, with heterogenous ERK and low pAkt levels promote survival, whereas high pAkt shifts towards apoptosis. Molecular perturbation analyses revealed a signaling hierarchy in which Akt dominates over AMPK which further dominates over ERK. This model further predicts that the extent of autophagy determines apoptotic outcomes with high autophagy favoring survival of matrix-detached MDA-MB-231 cells. Together, our study provides a mathematical framework linking signaling dynamics to cell-fate decisions governing anoikis resistance. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=147 HEIGHT=200 SRC="FIGDIR/small/658583v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@d40fdorg.highwire.dtl.DTLVardef@25a839org.highwire.dtl.DTLVardef@475401org.highwire.dtl.DTLVardef@dc4e6b_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2025

Chronic Inflammation Induced Immature Neutrophils Drive Immunopathology During Subsequent Inflammatory Events

Individuals with underlying chronic inflammatory conditions are prone to increased morbidity when posed with an additional inflammatory challenge such as an injury or infection, but why this occurs remains unclear. Herein, we address this question in mouse models by demonstrating that chronic inflammation results in a pronounced expansion of circulating immature neutrophils that exhibit dysregulated effector functions as determined by single cell RNA sequencing and ex vivo functional assays. We show that these immature neutrophils are associated with and contribute to increased immunopathology in response to a new inflammatory challenge. Blocking the migration or function of these immature neutrophils through the administration of therapeutic antibodies or small molecules, profoundly lowers the immunopathology caused by the inflammatory challenge. Together, these studies establish a causal link between immature neutrophils and increased immunopathology, while also providing insights into new therapeutic strategies for treating individuals with chronic inflammatory ailments.

immunology↗

bioRxiv2024

Hydrogen sulfide (H2S) coordinates redox balance, carbon metabolism, and mitochondrial bioenergetics to suppress SARS-CoV-2 infection.

Viruses exploit host metabolism for replication and immune-regulation. Understanding how SARS-CoV-2 alters the host metabolism may lead to treatments for COVID-19. We report that a ubiquitous gaseous molecule, hydrogen sulfide (H2S), regulates redox, metabolism, and mitochondrial bioenergetics to control SARS-CoV-2. Virus replication is associated with down-regulation of the H2S-producing enzymes cystathionine-{beta}-synthase (CBS), cystathionine-{gamma}-lyase (CTH), and 3-mercaptopyruvate sulfurtransferase (3-MST), resulting in diminished endogenous H2S levels. Inhibition of CTH resulted in SARS-CoV-2 proliferation. A slow-releasing H2S donor, GYY4137, diminished virus replication by inducing Nrf2/Keap1 pathway, restoring redox balance and mitochondrial bioenergetics. Treatment of SARS-CoV-2-infected animals with GYY4137 suppressed viral replication, ameliorated respiratory pathology, and restored antioxidant gene expression. Notably, whole-body plethysmography showed improved pulmonary function variables, including pulmonary obstruction and end-expiratory pause upon GYY4137 treatment in vivo. Data extend our understanding of H2S-mediated regulation of viral-infections, and open new avenues for investigating the pathogenic mechanisms and therapeutic opportunities for coronavirus-associated disorders.

microbiology↗

bioRxiv2024

Increased 'selfness' in the tumor emerges as a possible immune sculpting mechanism: A pan-cancer data analysis of 32 solid tumors in TCGA

Tumors pose a unique challenge to the immune system since they straddle the boundary between self and non-self. T-cells recognize tumors that contain non-self neo-antigens. They can also recognize tumors that contain aberrantly expressed self-antigens, highlighting the importance of the central tolerance and the tuning of the T-cell repertoire in the thymus. Therefore, the similarity to the thymic expression profiles must have information in it to influence the T-cell repertoire and what self-peptides are recognized. We utilize this principle in a pan-cancer analysis and develop a thymus-like or selfness score (TLS) based on the gene-expression similarity to thymi, indicative of recognizability of tumors by T-cells. We show that the TLS is indicative of patient survival in 8 different TCGA cohorts, indicating gene expression modulation to mimic that in thymi as a potential immune sculpting mechanism. Surprisingly, we also see an inverse relationship between TLS and the degree of immune infiltration.

immunology↗

bioRxiv2023

CRD: a De novo Design algorithm for prediction of Cognate Protein Receptors for small molecule ligands

While predicting a new ligand to bind to a protein is possible with current methods, the converse of predicting a receptor for a ligand is highly challenging, except for very closely-related known protein-ligand complexes. Predicting a receptor for any given ligand will be path-breaking in understanding protein function, mapping sequence-structure-function relationships and for several aspects of drug discovery including studying the mechanism of action of phenotypically discovered drugs, off-target effects and drug repurposing. We use a novel approach for predicting receptors for a given ligand through de novo design combined with structural bioinformatics. We have developed a new algorithm CRD, that has multiple modules which combines fragment-based sub-site finding, a machine learning function to estimate the size of the site, a genetic algorithm that encodes knowledge on protein structures and a physics-based fitness scoring scheme. CRD has a pseudo-receptor design component followed by a mapping component to identify possible proteins that house the site. CRD is designed to cater to ligands with known and unknown complexes. CRD accurately recovers sites and receptors for several known natural ligands including ATP, SAM, Glucose and FAD. It designs similar sites for similar ligands, yet to some extent distinguishes between closely related ligands. More importantly CRD correctly predicts receptor classes for several drugs such as penicillins and NSAIDs. We expect CRD to be a valuable tool in fundamental biology research as well as in the drug discovery and biotechnology industry.

bioinformatics↗

bioRxiv2022

Regenerative Agriculture Augments Bacterial Community Structure for a Healthier Soil and Agriculture

Use of chemical fertilization and pesticides not only harm the environment but also have detrimental consequences on human health. In recent years, there has been a major emphasis worldwide on natural agriculture methods. Regenerative agriculture is known across the world as a combination of nature-friendly farming practices such as no-till, cover cropping, crop-rotation, agro-forestry and use of organic home-based/farm-based ingredients to revive soil health. In India, a number of farmers are slowly adopting these practices using home-based mixtures and farmyard manure for soil rejuvenation and pest management. In order to evaluate the efficacy of the regenerative agriculture practices, this study compared conventional and regenerative agriculture plots for their soil bacterial and nutrient profiles. Two crops - ragi and vegetable (tomato/beans), and different lengths ([≤]3 and >5 years) of regenerative practices were additional metrics considered to understand variabilities due to crop-type and period of application. We found that all regenerative practices were effective in bringing about an enrichment for soil bacteria with a more heterogeneous composition. Additionally, the regenerative vegetable (RV) plots had an enhanced representation of Actinobacteriota, Chloroflexi, Cyanobacteria and Patescibacteria in comparison to conventional vegetable (CV) plots and Barren land (BL). Similarly, the regenerative ragi (RR) plots saw higher representation of Firmicutes and Actinobacteriota in comparison to conventional ragi (CR) plots and BL. The RV plots were also found to be enriched for Plant Growth Promoting Rhizobacteria (PGPRs) - Pseudomonas sp., and RR plots were enriched for Bacillus sp., and Mesorhizobium sp., which are known to play significant roles in vegetable and ragi growth respectively. Interestingly, long-term regenerative agriculture was able to support good nutrient composition while enhancing Soil Organic Carbon (SOC) levels. In all, the regenerative agriculture practices were found to be effective in improving bacterial community structure and simultaneously improving soil health. We found that BL soil with eucalyptus plantation showed least bacterial diversity suggesting detrimental impact on soil health.

ecology↗

bioRxiv2022

Functional connectivity across the human subcortical auditory system using a Gaussian copula graphical model approach with partial correlations

Abstract/SummaryThe auditory system comprises multiple subcortical brain structures that process and refine incoming acoustic signals along the primary auditory pathway. Due to technical limitations of imaging small structures deep inside the brain, most of our knowledge of the subcortical auditory system is based on research in animal models using invasive methodologies. Advances in ultra-high field functional magnetic resonance imaging (fMRI) acquisition have enabled novel non-invasive investigations of the human auditory subcortex, including fundamental features of auditory representation such as tonotopy and periodotopy. However, functional connectivity across subcortical networks is still underexplored in humans, with ongoing development of related methods. Traditionally, functional connectivity is estimated from fMRI data with full correlation matrices. However, partial correlations reveal the relationship between two regions after removing the effects of all other regions, reflecting more direct connectivity. Partial correlation analysis is particularly promising in the ascending auditory system, where sensory information is passed in an obligatory manner, from nucleus to nucleus up the primary auditory pathway, providing redundant but also increasingly abstract representations of auditory stimuli. While most existing methods for learning conditional dependency structures based on partial correlations assume independently and identically Gaussian distributed data, fMRI data exhibit significant deviations from Gaussianity as well as high temporal autocorrelation. In this paper, we developed an autoregressive matrix-Gaussian copula graphical model (ARMGCGM) approach to estimate the partial correlations and thereby infer the functional connectivity patterns within the auditory system while appropriately accounting for autocorrelations between successive fMRI scans. Our results show strong positive partial correlations between successive structures in the primary auditory pathway on each side (left and right), including between auditory midbrain and thalamus, and between primary and associative auditory cortex. These results are highly stable when splitting the data in halves according to the acquisition schemes and computing partial correlations separately for each half of the data, as well as across cross-validation folds. In contrast, full correlation-based analysis identified a rich network of interconnectivity that was not specific to adjacent nodes along the pathway. Overall, our results demonstrate that unique functional connectivity patterns along the auditory pathway are recoverable using novel connectivity approaches and that our connectivity methods are reliable across multiple acquisitions.

neuroscience↗

bioRxiv2022

Fast Local Alignment of Protein Pockets (FLAPP): A system-compiled program for large-scale binding site alignment

Protein function is a direct consequence of its sequence, structure and the arrangement at the binding site. Bioinformatics using sequence analysis is typically used to gain a first insight into protein function. Protein structures, on the other hand, provide a higher resolution platform into understanding functions. As the protein structural information is increasingly becoming available through experimental structure determination and through advances in computational methods for structure prediction, the opportunity to utilize this data is also increasing. Structural analysis of small molecule ligand binding sites in particular provide a direct and more accurate window to infer protein function. However it remains a poorly utilized resource due to the huge computational cost of existing methods that make large scale structural comparisons of binding sites prohibitive. Here we present an algorithm called FLAPP that produces very rapid atomic level alignments. By combining clique matching in graphs and the power of modern CPU architectures, FLAPP aligns a typical pair of binding site binding sites at ~12.5 milliseconds using a single CPU core, ~ 1 millisecond using 12 cores on a standard desktop machine, and performs a PDB-wide scan in 1-2 minutes. We perform rigorous validation of the algorithm at multiple levels of complexity and show that FLAPP provides accurate alignments. We also present a case study involving vitamin B12 binding sites to showcase the usefulness of FLAPP for performing an exhaustive alignment based PDB-wide scan. We expect this tool will be invaluable to the scientific community to quickly align millions of site pairs on a normal desktop machine to gain insights into protein function and drug discovery for drug target and off-target identification, and polypharmacology.

bioinformatics↗

bioRxiv2022

Moxifloxacin-mediated killing of Mycobacterium tuberculosis involves respiratory downshift, reductive stress, and ROS accumulation

Moxifloxacin is central to treatment of multidrug-resistant tuberculosis. Effects of moxifloxacin on Mycobacterium tuberculosis redox state were explored to identify strategies for increasing lethality and reducing the prevalence of extensively resistant tuberculosis. A non-invasive redox biosensor and an ROS-sensitive dye revealed that moxifloxacin induces oxidative stress correlated with M. tuberculosis death. Moxifloxacin lethality was mitigated by supplementing bacterial cultures with an ROS scavenger (thiourea), an iron chelator (bipyridyl), and, after drug removal, an antioxidant enzyme (catalase). Lethality was also reduced by hypoxia and nutrient starvation. Moxifloxacin increased the expression of genes involved in the oxidative stress response, iron-sulfur cluster biogenesis, and DNA repair. Surprisingly, and in contrast with Escherichia coli studies, moxifloxacin decreased expression of genes involved in respiration, suppressed oxygen consumption, increased the NADH/NAD+ ratio, and increased the labile iron pool in M. tuberculosis. Lowering the NADH/NAD+ ratio in M. tuberculosis revealed that NADH-reductive stress facilitates an iron-mediated ROS surge and moxifloxacin lethality. Treatment with N-acetyl cysteine (NAC) accelerated respiration and ROS production, increased moxifloxacin lethality, and lowered the mutant prevention concentration. Moxifloxacin induced redox stress in M. tuberculosis inside macrophages, and co-treatment with NAC potentiated the anti-mycobacterial efficacy of moxifloxacin during nutrient starvation, inside macrophages, and in mice where NAC restricted the emergence of resistance. Thus, oxidative stress, generated in a novel way, contributes to moxifloxacin-mediated killing of M. tuberculosis. The results open a way to make fluoroquinolones more effective anti-tuberculosis agents and provide a mechanistic basis for NAC-mediated enhancement of fluoroquinolone lethality in vitro and in vivo. Author Summary A new paradigm was revealed for stress-mediated bacterial death in which moxifloxacin treatment of M. tuberculosis decreases respiration rate (respiration increases in E. coli). Although moxifloxacin-induced, ROS-mediated bacterial death was observed, it derived from elevated levels of NADH and iron, a phenomenon not seen with antibiotic-treated E. coli. Nevertheless, stimulation of respiration and ROS by N-acetyl cysteine (NAC) enhanced moxifloxacin-mediated killing of M. tuberculosis, thereby reinforcing involvement of ROS in killing. NAC stimulation of moxifloxacin-mediated killing of M. tuberculosis and restriction of the emergence of resistance in a murine model of infection emphasize the importance of lethal action against pathogens. The work, plus published benefits of NAC to TB patients, encourage studies of NAC-based enhancement of fluoroquinolones.

microbiology↗

bioRxiv2021

Combinatorial transcriptional codes specify macrophage polarization destinations

Macrophages are driven to form distinct functional phenotypes in response to different immunological stimuli, in a process widely referred to as macrophage polarization. Transcriptional regulators that guide macrophage polarization in response to a given trigger remain largely unknown. In this study, we interrogate the programmable landscape in macrophages to find regulatory panels that determine the precise polarization state that a macrophage is driven to. Towards this, we configure an integrative network analysis pipeline that utilizes macrophage transcriptomes in response to 28 distinct stimuli and reconstructs contextualized human gene regulatory networks, and identifies epicentres of perturbations in each case. We find that these contextualized regulatory networks form a spectrum of thirteen distinct clusters with M1 and M2 at the two ends. Using our computational pipeline, we identify combinatorial panels of epicentric regulatory factors (RFs) for each polarization state. We demonstrate that a set of three RFs i.e., CEBPB, NFE2L2 and BCL3, is sufficient to change the polarization destination from M1 to M2. siRNA knockdown of the 3-RF set in THP1 derived M0 cells, despite exposure to an M1 stimulant, significantly attenuated the shift to M1 phenotype, and instead increased the expression of M2 markers. Single knockdown of each RF also showed a similar trend. The siRNA-mediated knockdown of the 3-RF set rendered the macrophages hyper-susceptible to Staphylococcus aureus infection, demonstrating the importance of these factors in modulating immune responses. Overall, our results provide insights into the transcriptional mechanisms underlying macrophage polarization and identify key regulatory factors that may be targeted to modulate immune responses.

systems biology↗

bioRxiv2020

PathExt: a general framework for path-based mining of omics-integrated biological networks

MotivationLarge scale transcriptomic data are routinely used to prioritize genes underlying specific phenotypes. Current approaches largely focus on differentially expressed genes (DEGs), despite the recognition that phenotypes emerge via a network of interactions between genes and proteins, many of which may not be differentially expressed. Furthermore, many practical applications lack sufficient samples or an appropriate control to robustly identify statistically significant DEGs. ResultsWe provide a computational tool - PathExt, which, in contrast to differential genes, identifies differentially active paths when a control is available, and most active paths otherwise, in an omics-integrated biological network. The sub-network comprising such paths, referred to as the Top-Net, captures the most relevant genes and processes underlying the specific biological context. The TopNet forms a well-connected graph, reflecting the tight orchestration in biological systems. Two key advantages of PathExt are (i) it can extract characteristic genes and pathways even when only a single sample is available, and (ii) it can be used to study a system even in the absence of an appropriate control. We demonstrate the utility of PathExt via two diverse sets of case studies, to characterize (a) Mycobacterium tuberculosis (M.tb) response upon exposure to 18 antibacterial drugs where only one transcriptomic sample is available for each exposure; and (b) tissue-relevant genes and processes using transcriptomic data from GTEx (Genotype-Tissue Expression) for 39 human tissues. Overall, PathExt is a general tool for prioritizing context-relevant genes in any omics-integrated biological network for any condition(s) of interest, even with a single sample or in the absence of appropriate controls. AvailabilityThe source code for PathExt is available at https://github.com/NarmadaSambaturu/PathExt. Contactnchandra@iisc.ac.in, sridhar.hannenhalli@nih.gov

systems biology↗

bioRxiv2019

A simple method to determine the elimination half-life of drugs displaying noncumulative toxicity

The pharmacokinetic characterization of a drug, especially the determination of its biological half-life, is an essential step during the early phases of drug development. An adequate half-life is amongst the many properties needed for selecting a drug candidate for clinical trials. Conversely, drug candidates possessing inadequate half-lives may be modified or eliminated from the drug discovery pipeline altogether. Several methods exist for determining the half-lives of drugs, namely HPLC, fluorescence assays, radioassays, radioimmunoassays, and elemental mass spectrometric assays. However, all these techniques are resource and labor-intensive, and cannot be used for the high-throughput half-life determination of hundreds of drug candidates. Here, we describe TOXHL: a simple technique to determine the half-lives of compounds displaying noncumulative toxicity. To calculate the half life, TOXHL only relies on the survival outcomes of three experiments performed on an animal model: an acute toxicity experiment, a cumulative toxicity experiment, and a multi-dose experiment at different dosing intervals. As a proof of concept, we use TOXHL to determine the peritoneal half-life of {Omega}76, an antimicrobial peptide. The half-life of {Omega}76 determined by TOXHL is in good agreement with results from a standard mass spectrometric method, validating this approach.

pharmacology and toxicology↗

bioRxiv2018

A uniform in vitro efficacy dataset to guide antimicrobial peptide design

Antimicrobial peptides are ubiquitous molecules that form the innate immune system of organisms across all kingdoms of life. Despite their prevalence and early origins, they continue to remain potent natural antimicrobial agents. Antimicrobial peptides are therefore promising drug candidates in the face of overwhelming multi-drug resistance to conventional antibiotics. Over the past few decades, thousands of antimicrobial peptides have been characterized in vitro, and their efficacy data is now available in a multitude of public databases. Computational antimicrobial peptide design attempts typically use such data. However, utilizing heterogenous data aggregated from different sources presents significant drawbacks. In this report, we present a uniform dataset containing 20 antimicrobial peptides assayed against 30 organisms spanning gram positive, gram negative, fungal, and mycobacterial origin. We draw inferences from the results of 600 individual MIC assays, and discuss what characteristics are essential for antimicrobial peptide efficacy. We expect our uniform dataset to be useful for future projects involving computational antimicrobial peptide design.

microbiology↗

bioRxiv2017

Redox-Dependent Condensation Of Mycobacterial Genome By WhiB4

Oxidative stress response in bacteria is generally mediated through coordination between the regulators of oxidant-remediation systems (e.g. OxyR, SoxR) and nucleoid condensation (e.g. Dps, Fis). However, these genetic factors are either absent or rendered nonfunctional in the human pathogen Mycobacterium tuberculosis (Mtb). Therefore, how Mtb organizes genome architecture and regulates gene expression to counterbalance oxidative imbalance during infection is not known. Here, we report that an intracellular redox-sensor, WhiB4, dynamically links genome condensation and oxidative stress response in Mtb. Disruption of WhiB4 affects the expression of genes involved in maintaining redox homeostasis, central carbon metabolism (CCM), respiration, cell wall biogenesis, DNA repair and protein quality control under oxidative stress. Notably, disulfide-linked oligomerization of WhiB4 in response to oxidative stress activates the proteins ability to condense DNA in vitro and in vivo. Further, overexpression of WhiB4 led to hypercondensation of nucleoids, redox imbalance and increased susceptibility to oxidative stress, whereas WhiB4 disruption reversed this effect. In accordance with the findings in vitro, ChIP-Seq data demonstrated non-specific binding of WhiB4 to GC-rich regions of the Mtb genome. Lastly, data indicate that WhiB4 deletion affected the expression of only a fraction of genes preferentially bound by the protein, suggesting its indirect effect on gene expression. We propose that WhiB4 is a novel redox-dependent nucleoid condensing protein that structurally couples Mtbs response to oxidative stress with genome organization and transcription.\n\nSignificance StatementMycobacterium tuberculosis (Mtb) needs to adapt in response to oxidative stress encountered inside human phagocytes. In other bacteria, condensation state of nucleoids modulates gene expression to coordinate oxidative stress response. However, this relation remains elusive in Mtb. We performed molecular dissection of a mechanism controlled by an intracellular redox sensor, WhiB4, in organizing both chromosomal structure and selective expression of adaptive traits to counter oxidative stress in Mtb. Using high-resolution sequencing, transcriptomics, imaging, and redox biosensor, we describe how WhiB4 modulates nucleoid condensation, global gene expression, and redox-homeostasis. WhiB4 over-expression hypercondensed nucleoids and perturbed redox homeostasis whereas WhiB4 disruption had an opposite effect. Our study discovered an empirical role for WhiB4 in integrating redox signals with nucleoid condensation in Mtb.

microbiology↗

bioRxiv2017

Efficacy of the β-lactam\β-lactamase inhibitor combination is linked to WhiB4 mediated changes in redox physiology of Mycobacterium tuberculosis

AimsInhibition of {beta}-lactamase by clavulanate (Clav) sensitizes multi-and extensively drug-resistant Mycobacterium tuberculosis (Mtb) strains towards {beta}-lactams such as amoxicillin (Amox). However, the underlying mechanism of how Mtb responds to Amox-Clav combination (Augmentin; AG) is not characterized.\n\nResultsWe integrated global expression profiling with the protein-protein interaction landscape and generated a genome-scale network of Mtb in response to AG. In addition to specific targets (e.g., peptidoglycan biosynthesis and {beta}-lactamase), the response to AG was also centered on redox-balance, central carbon metabolism (CCM), and respiration in Mtb. We discovered that AG modulates superoxide levels, NADH/NAD+ balance and mycothiol redox potential (EMSH) of Mtb. Higher intra-mycobacterial EMSH potentiates mycobactericidal efficacy of AG, whereas lower EMSH induces tolerance. Further, Mtb responds to AG via a redox-sensitive transcription factor, WhiB4. Mtb{Delta}whiB4 displayed higher expression of genes involved in {beta}-lactam resistance along with those mediating respiration, CCM and redox balance. Moreimportantly, WhiB4 binds to the promoter regions and represses transcription of genes involved in {beta}-lactamase expression in a redox-dependent manner. Lastly, while Mtb{Delta}whiB4 maintained internal EMSH, exhibited greater {beta}-lactamase activity and displayed AG-tolerance, overexpression of WhiB4 induced oxidative shift in EMSH and repressed {beta}-lactamase activity to aggravate AG-mediated killing of drug-sensitive and -resistant strains of Mtb.\n\nInnovation and ConclusionsThis work demonstrate that efficacy of {beta}-lactam\\{beta}-lactamase inhibitor combination can be attenuated by elevating mycobacterial antioxidant capabilities and potentiated by impairing redox buffering capacity of Mtb. The functional linkage between {beta}-lactams, redox balance, and WhiB4 can be exploited to potentiate AG action against drug-resistant Mtb.

microbiology↗