Phosphorylation of CFP10 modulates Mycobacterium tuberculosis virulence.

IMPORTANCE: Secreted virulence factors play a critical role in bacterial pathogenesis. Virulence effectors not only help bacteria to overcome the host immune system but also aid in establishing infection. Mtb, which causes tuberculosis in humans, encodes various virulence effectors. Triggers that modulate the secretion of virulence effectors in Mtb are yet to be fully understood. To gain mechanistic insight into the secretion of virulence effectors, we performed high-throughput proteomic studies. With the help of system-level protein-protein interaction network analysis and empirical validations, we unravelled a link between phosphorylation and secretion. Taking the example of the well-known virulence factor of CFP10, we show that the dynamics of CFP10 phosphorylation strongly influenced bacterial virulence and survival ex vivo and in vivo. This study presents the role of phosphorylation in modulating the secretion of virulence factors.

The heparin-binding hemagglutinin protein of Mycobacterium tuberculosis is a nucleoid-associated protein.

Nucleoid-associated proteins (NAPs) regulate multiple cellular processes such as gene expression, virulence, and dormancy throughout bacterial species. NAPs help in the survival and adaptation of Mycobacterium tuberculosis (Mtb) within the host. Fourteen NAPs have been identified in Escherichia coli; however, only seven NAPs are documented in Mtb. Given its complex lifestyle, it is reasonable to assume that Mtb would encode for more NAPs. Using bioinformatics tools and biochemical experiments, we have identified the heparin-binding hemagglutinin (HbhA) protein of Mtb as a novel sequence-independent DNA-binding protein which has previously been characterized as an adhesion molecule required for extrapulmonary dissemination. Deleting the carboxy-terminal domain of HbhA resulted in a complete loss of its DNA-binding activity. Atomic force microscopy showed HbhA-mediated architectural modulations in the DNA, which may play a regulatory role in transcription and genome organization. Our results showed that HbhA colocalizes with the nucleoid region of Mtb. Transcriptomics analyses of a hbhA KO strain revealed that it regulates the expression of ∼36% of total and ∼29% of essential genes. Deletion of hbhA resulted in the upregulation of ∼73% of all differentially expressed genes, belonging to multiple pathways suggesting it to be a global repressor. The results show that HbhA is a nonessential NAP regulating gene expression globally and acting as a plausible transcriptional repressor.

The PPE2 protein of Mycobacterium tuberculosis is secreted during infection and facilitates mycobacterial survival inside the host.

Mycobacterium tuberculosis secrets various effector proteins to evade host immune responses for facilitating its intracellular survival. The bacterial genome encodes several unique PE/PPE family proteins, which have been implicated to play important role in mycobacterial pathogenesis. A member of this family, PPE2 have been shown to contain a monopartite nuclear localization signal (NLS) and a DNA binding domain. In this study, we demonstrate that PPE2 protein is present in the sera of mice infected with either M. smegmatis expressing PPE2 or a clinical strain of M. tuberculosis (CDC1551). It was found that exogenously added PPE2 can permeate through the macrophage cell membrane and eventually translocate into the nucleus which requires the presence of NLS which showed considerable homology to HIV-tat like cell permeable peptides. Exogenously added PPE2 could inhibit NO production and decreased mycobacterial survival in macrophages. PPE2-null mutant of M. tuberculosis failed to inhibit NO production and had poor survival in macrophages which could be rescued by complementation with full-length PPE2. PPE2-null mutants also had poor survival in the lungs of infected mice indicating that PPE2 even when present in the bloodstream can confer a survival advantage to mycobacteria.

Synthesis, Structural Elucidation and Pharmacological Applications of Cu(II) Heteroleptic Carboxylates.

Six heteroleptic Cu(II) carboxylates (1-6) were prepared by reacting 2-chlorophenyl acetic acid (L1), 3-chlorophenyl acetic acid (L2), and substituted pyridine (2-cyanopyridine and 2-chlorocyanopyridine). The solid-state behavior of the complexes was described via vibrational spectroscopy (FT-IR), which revealed that the carboxylate moieties adopted different coordination modes around the Cu(II) center. A paddlewheel dinuclear structure with distorted square pyramidal geometry was elucidated from the crystal data for complexes 2 and 5 with substituted pyridine moieties at the axial positions. The presence of irreversible metal-centered oxidation reduction peaks confirms the electroactive nature of the complexes. A relatively higher binding affinity was observed for the interaction of SS-DNA with complexes 2-6 compared to L1 and L2. The findings of the DNA interaction study indicate an intercalative mode of interaction. The maximum inhibition against acetylcholinesterase enzyme was caused for complex 2 (IC50 = 2 µg/mL) compared to the standard drug Glutamine (IC50 = 2.10 µg/mL) while the maximum inhibition was found for butyrylcholinesterase enzyme by complex 4 (IC50 = 3 µg/mL) compared to the standard drug Glutamine (IC50 = 3.40 µg/mL). The findings of the enzymatic activity suggest that the under study compounds have potential for curing of Alzheimer's disease. Similarly, complexes 2 and 4 possess the maximum inhibition as revealed from the free radical scavenging activity performed against DPPH and H2O2.

GWAS and functional studies suggest a role for altered DNA repair in the evolution of drug resistance in Mycobacterium tuberculosis.

The emergence of drug resistance in Mycobacterium tuberculosis (Mtb) is alarming and demands in-depth knowledge for timely diagnosis. We performed genome-wide association analysis using 2237 clinical strains of Mtb to identify novel genetic factors that evoke drug resistance. In addition to the known direct targets, we identified for the first time, a strong association between mutations in DNA repair genes and the multidrug-resistant phenotype. To evaluate the impact of variants identified in the clinical samples in the evolution of drug resistance, we utilized knockouts and complemented strains in Mycobacterium smegmatis and Mtb. Results show that variant mutations compromised the functions of MutY and UvrB. MutY variant showed enhanced survival compared with wild-type (Rv) when the Mtb strains were subjected to multiple rounds of ex vivo antibiotic stress. In an in vivo guinea pig infection model, the MutY variant outcompeted the wild-type strain. We show that novel variant mutations in the DNA repair genes collectively compromise their functions and contribute to better survival under antibiotic/host stress conditions.

Protocol for ex vivo competition and sequencing of mycobacterium isolated from infected guinea pigs.

We describe steps for gDNA isolation from mycobacterium strains isolated from guinea pig lungs. We detail steps for infection of guinea pigs with Mycobacterium tuberculosis, followed by in vitro growth, gDNA isolation, and whole genome sequencing. We also describe an ex vivo competition experiment to determine the selective advantage of one strain over another. We include details for WGS and mutation spectrum analysis. The protocol can be used to identify mutations that arise in other pathogenic bacteria. For complete details on the use and execution of this protocol, please refer to Naz et al. (2021).

The Error-Prone Polymerase DnaE2 Mediates the Evolution of Antibiotic Resistance in Persister Mycobacterial Cells.

Applying antibiotics to susceptible bacterial cultures generates a minor population of persisters that remain susceptible to antibiotics but can endure them for extended periods. Recent reports suggest that antibiotic persisters (APs) of mycobacteria experience oxidative stress and develop resistance upon treatment with lethal doses of ciprofloxacin or rifampicin. However, the mechanisms driving the de novo emergence of resistance remained unclear. Here, we show that mycobacterial APs activate the SOS response, resulting in the upregulation of the error-prone DNA polymerase DnaE2. The sustained expression of dnaE2 in APs led to mutagenesis across the genome and resulted in the rapid evolution of resistance to antibiotics. Inhibition of RecA by suramin, an anti-Trypanosoma drug, reduced the rate of conversion of persisters to resistors in a diverse group of bacteria. Our study highlights suramin's novel application as a broad-spectrum agent in combating the development of drug resistance.

Chromatographic evaluation of tocols and sterols of processed canola oil and deodorizer distillate.

Tocopherols and tocotrienols in the combined form are known as tocols. Changes of total and individual tocols and sterols concentration of canola oil and deodorizer distillate (DD) during different processing stages were evaluated with the application of gas chromatography (GC) and high-performance liquid chromatography (HPLC). For sterols analysis, GC coupled with flame ionization detector (FID) was used while tocols in canola oil samples and DD, normal phase (NP) HPLC was applied. The results of the present study indicated that levels of total and individual tocols and sterols content were decreased during processing (neutralization to deodorization). Deodorization was found to be the most effective process for the reduction of total sterols and tocols as 55.9% and 34.2%, respectively. A high amount of tocols and sterols was observed in DD. Among tocols and sterols; beta tocopherol (ß-T) and ß-sitosterol were found to be in greater concentration 53.97% and 31.82%, respectively. Therefore, DD could be used as a valuable by-product in the cosmetics and food industries.

Compromised base excision repair pathway in Mycobacterium tuberculosis imparts superior adaptability in the host.

Tuberculosis caused by Mycobacterium tuberculosis (Mtb) is a significant public health concern, exacerbated by the emergence of drug-resistant TB. To combat the host's dynamic environment, Mtb encodes multiple DNA repair enzymes that play a critical role in maintaining genomic integrity. Mtb possesses a GC-rich genome, rendering it highly susceptible to cytosine deaminations, resulting in the occurrence of uracils in the DNA. UDGs encoded by ung and udgB initiate the repair; hence we investigated the biological impact of deleting UDGs in the adaptation of pathogen. We generated gene replacement mutants of uracil DNA glycosylases, individually (RvΔung, RvΔudgB) or together (RvΔdKO). The double KO mutant, RvΔdKO exhibited remarkably higher spontaneous mutation rate, in the presence of antibiotics. Interestingly, RvΔdKO showed higher survival rates in guinea pigs and accumulated large number of SNPs as revealed by whole-genome sequence analysis. Competition assays revealed the superior fitness of RvΔdKO over Rv, both in ex vivo and in vivo conditions. We propose that compromised DNA repair results in the accumulation of mutations, and a subset of these drives adaptation in the host. Importantly, this property allowed us to utilize RvΔdKO for the facile identification of drug targets.

Deletion of serine/threonine-protein kinase pknL from Mycobacterium tuberculosis reduces the efficacy of isoniazid and ethambutol.

Serine/threonine-protein kinases in Mycobacterium tuberculosis (Mtb) form a preeminent regulatory system required to establish and maintain the infection in the host. Herein, we sought to decipher the biological role of PknL with the help of a gene replacement mutant RvΔpknL. Deletion of pknL results in the compromised growth under redox stress. The mutant showed significant survival defects in peritoneal macrophages, a significant decrease in the ability to establish infections and disseminate to the spleen in the murine model of infection. While the absence of pknL has no impact on either MIC or CFUs of ciprofloxacin and rifampicin treated bacilli, it increases the survival ~1.5-2.5 log fold upon isoniazid or ethambutol treatment. Collectively, data suggests that PknL aids in combating stress conditions in vitro, ex vivo, and in vivo and reduces the efficacy of isoniazid and ethambutol.

Methylation of two-component response regulator MtrA in mycobacteria negatively modulates its DNA binding and transcriptional activation.

Post-translational modifications such as phosphorylation, nitrosylation, and pupylation modulate multiple cellular processes in Mycobacterium tuberculosis. While protein methylation at lysine and arginine residues is widespread in eukaryotes, to date only two methylated proteins in Mtb have been identified. Here, we report the identification of methylation at lysine and/or arginine residues in nine mycobacterial proteins. Among the proteins identified, we chose MtrA, an essential response regulator of a two-component signaling system, which gets methylated on multiple lysine and arginine residues to examine the functional consequences of methylation. While methylation of K207 confers a marginal decrease in the DNA-binding ability of MtrA, methylation of R122 or K204 significantly reduces the interaction with the DNA. Overexpression of S-adenosyl homocysteine hydrolase (SahH), an enzyme that modulates the levels of S-adenosyl methionine in mycobacteria decreases the extent of MtrA methylation. Most importantly, we show that decreased MtrA methylation results in transcriptional activation of mtrA and sahH promoters. Collectively, we identify novel methylated proteins, expand the list of modifications in mycobacteria by adding arginine methylation, and show that methylation regulates MtrA activity. We propose that protein methylation could be a more prevalent modification in mycobacterial proteins.

Synthesis of nickel nanoparticles using Citrullus colocynthis stem extract for remediation of Reactive Yellow 160 dye.

In current years, pollution caused by synthetic dyes has become one of the most serious environmental issues. By rapidly developing industrial units, effluents having synthetic dyes are directly or indirectly being discharged into the environment. Bio-sorption is cost-effective way for the eradication of toxic dyes present in textile effluent. The present study involves the synthesis of nickel nanoparticles using Citrullus colocynthis stem extract. The characterization of synthesized nickel nanoparticles (Ni-NPs) was done by SEM. The synthesized Ni-NPs were used to degrade the Reactive Yellow 160 dye following the optimization of different experimental parameters. The maximum decolorization (91.4%) was obtained at 0.02% dye conc., 9 mg/L conc. of Ni-NPs, pH 7 at 40 °C. TOC and COD were used to assess the efficiency of this experiment. Percent reduction in COD and TOC was found to be 84.35% and 83.24% respectively. The degradation pathway of dye under study confirmed the formation of non-toxic end-products.

Tuning the Mycobacterium tuberculosis Alternative Sigma Factor SigF through the Multidomain Regulator Rv1364c and Osmosensory Kinase Protein Kinase D.

Bacterial alternative sigma factors are mostly regulated by a partner-switching mechanism. Regulation of the virulence-associated alternative sigma factor SigF of Mycobacterium tuberculosis has been an area of intrigue, with SigF having more predicted regulators than other sigma factors in this organism. Rv1364c is one such predicted regulator, the mechanism of which is confounded by the presence of both anti-sigma factor and anti-sigma factor antagonist functions in a single polypeptide. Using protein binding and phosphorylation assays, we demonstrate that the anti-sigma factor domain of Rv1364c mediates autophosphorylation of its antagonist domain and binds efficiently to SigF. Furthermore, we identified a direct role for the osmosensor serine/threonine kinase PknD in regulating the SigF-Rv1364c interaction, adding to the current understanding about the intersection of these discrete signaling networks. Phosphorylation of SigF also showed functional implications in its DNA binding ability, which may help in activation of the regulon. In M. tuberculosis, osmotic stress-dependent induction of espA, a SigF target involved in maintaining cell wall integrity, is curtailed upon overexpression of Rv1364c, showing its role as an anti-SigF factor. Overexpression of Rv1364c led to induction of another target, pks6, involved in lipid metabolism. This induction was, however, curtailed in the presence of osmotic stress conditions, suggesting modulation of SigF target gene expression via Rv1364c. These data provide evidence that Rv1364c acts an independent SigF regulator that is sensitive to the osmosensory signal, mediating the cross talk of PknD with the SigF regulon.IMPORTANCEMycobacterium tuberculosis, capable of latently infecting the host and causing aggressive tissue damage during active tuberculosis, is endowed with a complex regulatory capacity built of several sigma factors, protein kinases, and phosphatases. These proteins regulate expression of genes that allow the bacteria to adapt to various host-derived stresses, like nutrient starvation, acidic pH, and hypoxia. The cross talk between these systems is not well understood. SigF is one such regulator of gene expression that helps M. tuberculosis to adapt to stresses and imparts virulence. This work provides evidence for its inhibition by the multidomain regulator Rv1364c and activation by the kinase PknD. The coexistence of negative and positive regulators of SigF in pathogenic bacteria reveals an underlying requirement for tight control of virulence factor expression.

Angioedema; An Unreported Adverse Effect Of Pitavastatin.

Angioedema is a life-threatening reaction characterized by swelling of the face, lips, tongue or larynx. Known adverse effects of Pitavastatin do not include angioedema. We report first case of a 55-year-old Asian male developing post exposure angioedema to 2 mg Pitavastatin. Note that the patient showed no history of hypersensitivity. Relationship between Pitavastatin and angioedema was assessed by Naranjo scale.

Mycobacterium tuberculosis EsxL inhibits MHC-II expression by promoting hypermethylation in class-II transactivator loci in macrophages.

Mycobacterium tuberculosis is known to modulate the host immune responses to facilitate its persistence inside the host cells. One of the key mechanisms includes repression of class-II transactivator (CIITA) and MHC-II expression in infected macrophages. However, the precise mechanism of CIITA and MHC-II down-regulation is not well studied. M. tuberculosis 6-kDa early secretory antigenic target (ESAT-6) is a known potent virulence and antigenic determinant. The M. tuberculosis genome encodes 23 such ESAT-6 family proteins. We herein report that M. tuberculosis and M. bovis bacillus Calmette-Guérin infection down-regulated the expression of CIITA/MHC-II by inducing hypermethylation in histone H3 lysine 9 (H3K9me2/3). Further, we showed that M. tuberculosis ESAT-6 family protein EsxL, encoded by Rv1198, is responsible for the down-regulation of CIITA/MHC-II by inducing H3K9me2/3. We further report that M. tuberculosis esxL induced the expression of nitric-oxide synthase, NO production, and p38 MAPK pathway, which in turn was responsible for the increased H3K9me2/3 in CIITA via up-regulation of euchromatic histone-lysine N-methyltransferase 2 (G9a). In contrast, inhibition of nitric-oxide synthase, p38 MAPK, and G9a abrogated H3K9me2/3, resulting in increased CIITA expression. A chromatin immunoprecipitation assay confirmed that hypermethylation at the promoter IV region of CIITA is mainly responsible for CIITA down-regulation and subsequent antigen presentation. We found that co-culture of macrophages infected with esxL-expressing M. smegmatis and mouse splenocytes led to down-regulation of IL-2, a key cytokine involved in T-cell proliferation. In summary, we demonstrate that M. tuberculosis EsxL inhibits antigen presentation by enhancing H3K9me2/3 at the CIITA promoter, thereby repressing its expression through NO and p38 MAPK activation.

Protein kinase A (PknA) of Mycobacterium tuberculosis is independently activated and is critical for growth in vitro and survival of the pathogen in the host.

The essential mycobacterial protein kinases PknA and PknB play crucial roles in modulating cell shape and division. However, the precise in vivo functional aspects of PknA have not been investigated. This study aims to dissect the role of PknA in mediating cell survival in vitro as well as in vivo. We observed aberrant cell shape and severe growth defects when PknA was depleted. Using the mouse infection model, we observe that PknA is essential for survival of the pathogen in the host. Complementation studies affirm the importance of the kinase, juxtamembrane, and transmembrane domains of PknA. Surprisingly, the extracytoplasmic domain is dispensable for cell growth and survival in vitro. We find that phosphorylation of the activation loop at Thr(172) of PknA is critical for bacterial growth. PknB has been previously suggested to be the receptor kinase, which activates multiple kinases, including PknA, by trans-phosphorylating their activation loop residues. Using phospho-specific PknA antibodies and conditional pknB mutant, we find that PknA autophosphorylates its activation loop independent of PknB. Fluorescently tagged PknA and PknB show distinctive distribution patterns within the cell, suggesting that although both kinases are known to modulate cell shape and division, their modes of action are likely to be different. This is supported by our findings that expression of kinase-dead PknA versus kinase-dead PknB in mycobacterial cells leads to different cellular phenotypes. Data indicate that although PknA and PknB are expressed as part of the same operon, they appear to be regulating cellular processes through divergent signaling pathways.

Application of multivariate chemometric techniques for simultaneous determination of five parameters of cottonseed oil by single bounce attenuated total reflectance Fourier transform infrared spectroscopy.

Single bounce attenuated total reflectance (SB-ATR) Fourier transform infrared (FTIR) spectroscopy in conjunction with chemometrics was used for accurate determination of free fatty acid (FFA), peroxide value (PV), iodine value (IV), conjugated diene (CD) and conjugated triene (CT) of cottonseed oil (CSO) during potato chips frying. Partial least square (PLS), stepwise multiple linear regression (SMLR), principal component regression (PCR) and simple Beer׳s law (SBL) were applied to develop the calibrations for simultaneous evaluation of five stated parameters of cottonseed oil (CSO) during frying of French frozen potato chips at 170°C. Good regression coefficients (R(2)) were achieved for FFA, PV, IV, CD and CT with value of >0.992 by PLS, SMLR, PCR, and SBL. Root mean square error of prediction (RMSEP) was found to be less than 1.95% for all determinations. Result of the study indicated that SB-ATR FTIR in combination with multivariate chemometrics could be used for accurate and simultaneous determination of different parameters during the frying process without using any toxic organic solvent.

Rapid determination of free fatty acid content in waste deodorizer distillates using single bounce-attenuated total reflectance-FTIR spectroscopy.

A simple, rapid, economical, and environmentally friendly analytical method was developed for the quantitative assessment of free fatty acids (FFAs) present in deodorizer distillates and crude oils by single bounce-attenuated total reflectance-FTIR spectroscopy. Partial least squares was applied for the calibration model based on the peak region of the carbonyl group (C=O) from 1726 to 1664 cm(-1) associated with the FFAs. The proposed method totally avoided the use of organic solvents or costly standards and could be applied easily in the oil processing industry. The accuracy of the method was checked by comparison to a conventional standard American Oil Chemists' Society (AOCS) titrimetric procedure, which provided good correlation (R = 0.99980), with an SD of +/- 0.05%. Therefore, the proposed method could be used as an alternate to the AOCS titrimetric method for the quantitative determination of FFAs especially in deodorizer distillates.