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

PhoP-PhoR, one of the 12 two-component systems (TCSs) that empower M. tuberculosis to sense and adapt to diverse environmental conditions, remains essential for virulence, and therefore, represents a major target to develop novel anti-TB therapies. Although both PhoP and PhoR have been structurally characterized, the signal(s) that this TCS responds to remains unknown. Here, we show that PhoR is a sensor of acidic pH/high salt conditions, which subsequently activate PhoP via phosphorylation. In keeping with this, transcriptomic data uncover that acidic pH- inducible expression of PhoP regulon is significantly inhibited in a PhoR-deleted M. tuberculosis. Strikingly, a set of PhoP regulon genes displayed a low pH-dependent activation even in the absence of PhoR, suggesting the presence of non-canonical mechanism(s) of PhoP activation. Using genome-wide interaction-based screening coupled with phosphorylation assays, we identify a non-canonical mechanism of PhoP phosphorylation by the sensor kinase PrrB. To investigate how level of P~PhoP is regulated, we discovered that in addition to its kinase activity PhoR functions as a phosphatase of P~PhoP. Our subsequent results identify the motif/residues responsible for kinase/phosphatase dual functioning of PhoR. Collectively, these results uncover that contrasting kinase and phosphatase functions of PhoR determine the homeostatic mechanism of regulation of intra-mycobacterial P~PhoP which controls the final output of the PhoP regulon. Together, these results connect PhoR to pH-dependent activation of PhoP with downstream functioning of the regulator. Thus, PhoR plays a central role in mycobacterial adaptation to low pH conditions within the host macrophage phagosome, and a PhoR-deleted M. tuberculosis remains significantly attenuated in macrophages and animal models.

Characterizing variability in total mercury hair:blood ratio in the general Canadian population.

BACKGROUND/OBJECTIVES: The body burden of mercury in humans can be measured through hair or blood biomarkers. To compare results from different studies, it is often required to convert mercury in hair to an equivalent level in blood, using a default hair:blood ratio of 250:1 by the World Health Organization (WHO). However, the actual ratio may vary within and between populations. The objectives of this study were to analyze the hair:blood mercury ratio in the general Canadian population, explore factors associated with higher/lower ratios, and determine if the standard ratio of 250:1 is supported. METHODS: The Canadian Health Measures Survey (CHMS) Cycle 5 (2016-2017) measured total mercury (THg) in both hair and blood of 1168 participants 20-59 years of age. We calculated geometric mean (GM) concentrations of THg for this entire sample and subgroups. The subgroups included biological sex, women of childbearing age, race, hair treatments, categories of blood and hair selenium, urinary arsenobetaine/arsenocholine, categories of blood and hair mercury, and food consumption. We calculated a hair:blood ratio for each participant and determined population-level ratios from the GMs of the distributions. Differences by subgroups, and agreement with the WHO ratio of 250:1, were tested. The combined effect of factors on the THg hair:blood ratio was explored using staged regression analysis. RESULTS: For participants with paired hair and blood mercury measurements, the GM of the hair:blood THg ratio was 293 (95%CI:273-316), and significantly >250. In women of childbearing age, the ratio did not differ from 250. The GMs of the ratio were higher (i.e.>300) for second tertile blood selenium (365, 95%CI:307-433), third and fourth quartiles hair mercury (347, 95%CI:308-390 and 376, 95%CI:336-422), and consumers of shellfish (338, 95%CI:308-371). Shellfish consumption was the only statistically significant factor associated with the hair:blood ratio as identified in the regression model. CONCLUSIONS: The mean hair:blood THg ratio among Canadians generally exceeded the default ratio of 250:1. Higher ratios were observed in certain subgroups, such as seafood consumers, and shellfish consumption was the most important variable associated with the ratio. Our results suggest that population-specific hair:blood THg ratios be considered, if possible, when converting mercury levels from hair to blood to better characterize the variation around the conversion.

Functioning of Mycobacterial Heat Shock Repressors Requires the Master Virulence Regulator PhoP.

A hallmark feature of Mycobacterium tuberculosis pathogenesis lies in the ability of the pathogen to survive within macrophages under a stressful environment. Thus, coordinated regulation of stress proteins is critically important for an effective adaptive response of M. tuberculosis, the failure of which results in elevated immune recognition of the tubercle bacilli with reduced survival during chronic infections. Here, we show that virulence regulator PhoP impacts the global regulation of heat shock proteins, which protect M. tuberculosis against stress generated by macrophages during infection. Our results identify that in addition to classical DNA-protein interactions, newly discovered protein-protein interactions control complex mechanisms of expression of heat shock proteins, an essential pathogenic determinant of M. tuberculosis While the C-terminal domain of PhoP binds to its target promoters, the N-terminal domain of the regulator interacts with the C-terminal end of the heat shock repressors. Remarkably, our findings delineate a regulatory pathway which involves three major transcription factors, PhoP, HspR, and HrcA, that control in vivo recruitment of the regulators within the target genes and regulate stress-specific expression of heat shock proteins via protein-protein interactions. The results have implications on the mechanism of regulation of PhoP-dependent stress response in M. tuberculosisIMPORTANCE The regulation of heat shock proteins which protect M. tuberculosis against stress generated by macrophages during infection is poorly understood. In this study, we show that PhoP, a virulence regulator of the tubercle bacilli, controls heat shock-responsive genes, an essential pathogenic determinant of M. tuberculosis Our results unravel that in addition to classical DNA-protein interactions, complex mechanisms of regulation of heat shock-responsive genes occur through multiple protein-protein interactions. Together, these findings delineate a fundamental regulatory pathway where transcription factors PhoP, HspR, and HrcA interact with each other to control stress-specific expression of heat shock proteins.

Synthesis of Strongly Fluorescent Imidazole Derivatives: Structure Property Studies, Halochromism and Fluorescent Photoswitching.

New series of methoxy and hydroxyl group substituted triphenylamine (TPA)-imidazole fluorescent molecules (5-(diphenylamino)-2-(1H-phenanthro[9,10-d]imidazol-2-yl)phenol (1), 5-(diphenylamino)-2-(1-phenyl-1H-phenanthro[9,10-d]imidazol-2-yl)phenol (2), 5-(diphenylamino)-2-(4,5-diphenyl-1H-imidazol-2-yl)phenol (3), 5-(diphenylamino)-2-(1,4,5-triphenyl-1H-imidazol-2-yl)phenol (4), N-(3-methoxy-4-(1H-phenanthro[9,10-d]imidazol-2-yl)phenyl)-N-phenylbenzenamine (5), N-(3-methoxy-4-(1-phenyl-1H-phenanthro[9,10-d]imidazol-2-yl)phenyl)-N-phenylbenzene amine (6), and N-(3-methoxy-4-(4,5-diphenyl-1H-imidazol-2-yl)phenyl)-N-phenylbenzenamine (7)) have been synthesized that exhibited strong solution fluorescence and molecular structure and conformation controlled fluorescence photoswitching, solid state fluorescence and halochromism. Hydroxyl substituted molecules (1-4) showed moderate to strong fluorescence in solution depend on solvent polarity and very weak solid state fluorescence. Methoxy substituted molecules (5-7) displayed strong fluorescence both in solution and solid state. Solid state structural studies revealed strong intramolecular H-bonding in the crystal lattice. Interestingly, highly twisted structure (6) showed rare light induced reversible fluorescence switching in CHCl3. The observation of isobestic point in time dependent fluorescence photoswitching studies indicated structural isomer conversion. Further, acid sensitive imidazole nitrogen has been made use to demonstrate solid state fluorescence switching via halochromism. Thus the present studies attempted to develop new fluorescent molecules and establish structure-property relationship for designing fluorescence switching materials. Graphical Abstract Molecular structure controlled solid state fluorescence, halochromism and a rare fluorescence photoswitching in chloroform have been observed with triphenylamine-imidazole derivatives.

Factors associated with plasma concentrations of polychlorinated biphenyls (PCBs) and dichlorodiphenyldichloroethylene (p,p'-DDE) in the Canadian population.

This study describes blood plasma concentrations of PCBs and p,p'-DDE in the Canadian population aged 20-79 years. PCBs and p,p'-DDE were measured in 1668 participants in the Canadian Health Measures Survey, Cycle 1 (2007-2009). We investigated how concentrations vary by sociodemographic, anthropometric, and lifestyle variables, identified factors associated with exposures, and evaluated concentrations against health-based guidance values. Congeners of PCB most commonly detected were PCB-138, PCB-153, and PCB-180. p,p'-DDE was detectable in > 99% of the samples. Factors associated with ∑PCBs were age, region of birth, frequency of fish consumption, and liver intake (R2 = 58.1%). For p,p'-DDE, significant factors were sex, age, region of birth, household education, and ethnic origin (R2 = 47.0%). PCB concentrations in Canadians were similar to those in the United States, and lower than those reported in Europe. A small percentage equalled or exceeded the Human Biomonitoring value of 3.5 µg/L for PCBs. Few exceedances of the p,p'-DDE biomonitoring equivalent were observed.

Structural characterization of ribT from Bacillus subtilis reveals it as a GCN5-related N-acetyltransferase.

In bacteria, biosynthesis of riboflavin occurs through a series of enzymatic steps starting with one molecule of GTP and two molecules of ribulose-5-phosphate. In Bacillus subtilis (B. subtilis) the genes (ribD/G, ribE, ribA, ribH and ribT) which are involved in riboflavin biosynthesis are organized in an operon referred as rib operon. All the genes of rib operon are characterized functionally except for ribT. The ribT gene with unknown function is found at the distal terminal of rib operon and annotated as a putative N-acetyltransferase. Here, we report the crystal structure of ribT from B. subtilis (bribT) complexed with coenzyme A (CoA) at 2.1 Šresolution determined by single wavelength anomalous dispersion method. Our structural study reveals that bribT is a member of GCN5-related N-acetyltransferase (GNAT) superfamily and contains all the four conserved structural motifs that have been in other members of GNAT superfamily. The members of GNAT family transfers the acetyl group from acetyl coenzyme A (AcCoA) to a variety of substrates. Moreover, the structural analysis reveals that the residues Glu-67 and Ser-107 are suitably positioned to act as a catalytic base and catalytic acid respectively suggesting that the catalysis by bribT may follow a direct transfer mechanism. Surprisingly, the mutation of a non-conserved amino acid residue Cys-112 to alanine or serine affected the binding of AcCoA to bribT, indicating a possible role of Cys-112 in the catalysis.

Phosphorylation of mycobacterial phosphodiesterase by eukaryotic-type Ser/Thr kinase controls its two distinct and mutually exclusive functionalities.

Phosphorylation-mediated negative feedback regulation of cAMP levels by phosphodiesterase is well-established in eukaryotic cells. However, such a mechanism remains unexplored in prokaryotes. We report here the involvement of eukaryotic-type Ser/Thr kinases, particularly PknA in trans-phosphorylating phosphodiesterase from Mycobacterium tuberculosis (mPDE), that resulted in decreased enzyme turnover rate compared with its unphosphorylated counterpart. To elucidate the role of mPDE phosphorylation in hydrolyzing cellular cAMP, we utilized a phosphodiesterase knock-out Escherichia coli strain, ΔcpdA, where interference of endogenous eukaryotic-type Ser/Thr kinases could be excluded. Interestingly, the mPDE-complemented ΔcpdA strain showed enhanced cAMP levels in the presence of PknA, and this effect was antagonized by PknA-K42N, a kinase-dead variant. Structural analysis of mPDE revealed that four Ser/Thr residues (Ser-20, Thr-22, Thr-182, and Thr-240) were close to the active site, indicating their possible role in phosphorylation-mediated alteration in enzymatic activity. Mutation of these residues one at a time to alanine or a combination of all four (mPDE-4A) affected catalytic activity of mPDE. Moreover, mPDE-4A protein in kinase assays exhibited reduction in its phosphorylation compared with mPDE. In consonance, phosphoproteins obtained after co-expression of PknA with mPDE/S20A/T240A/4A displayed decreased phospho-signal intensities in immunoblotting with anti-phosphoserine/phosphothreonine antibodies. Furthermore, unlike mPDE, phospho-ablated mPDE-T309A protein exhibited impaired cell wall localization in Mycobacterium smegmatis, whereas mPDE-4A behaved similarly as wild type. Taken together, our findings establish mutually exclusive dual functionality of mPDE upon PknA-mediated phosphorylation, where Ser-20/Thr-240 influence enzyme activity and Thr-309 endorses its cell wall localization.

ChaC2, an Enzyme for Slow Turnover of Cytosolic Glutathione.

Glutathione degradation plays an important role in glutathione and redox homeostasis, and thus it is imperative to understand the enzymes and the mechanisms involved in glutathione degradation in detail. We describe here ChaC2, a member of the ChaC family of γ-glutamylcyclotransferases, as an enzyme that degrades glutathione in the cytosol of mammalian cells. ChaC2 is distinct from the previously described ChaC1, to which ChaC2 shows ∼50% sequence identity. Human and mouse ChaC2 proteins purified in vitro show 10-20-fold lower catalytic efficiency than ChaC1, although they showed comparable Km values (Km of 3.7 ± 0.4 mm and kcat of 15.9 ± 1.0 min-1 toward glutathione for human ChaC2; Km of 2.2 ± 0.4 mm and kcat of 225.2 ± 15 min-1 toward glutathione for human ChaC1). The ChaC1 and ChaC2 proteins also shared the same specificity for reduced glutathione, with no activity against either γ-glutamyl amino acids or oxidized glutathione. The ChaC2 proteins were found to be expressed constitutively in cells, unlike the tightly regulated ChaC1. Moreover, lower eukaryotes have a single member of the ChaC family that appears to be orthologous to ChaC2. In addition, we determined the crystal structure of yeast ChaC2 homologue, GCG1, at 1.34 Å resolution, which represents the first structure of the ChaC family of proteins. The catalytic site is defined by a fortuitous benzoic acid molecule bound to the crystal structure. The mechanism for binding and catalytic activity of this new enzyme of glutathione degradation, which is involved in continuous but basal turnover of cytosolic glutathione, is proposed.

Unusual fluorescent photoswitching of imidazole derivatives: the role of molecular conformation and twist angle controlled organic solid state fluorescence.

Molecular photoswitching, light induced reversible color/fluorescence modulation, has mostly been realized in organic molecules via E/Z isomerization of azobenzenes and stilbenes and ring opening/closing reactions of spiropyrans and diarylethenes. We report here new fluorescent molecular photoswitches based on triphenylamine (TPA)-imidazole derivatives, N-phenyl-N-(4-(1,4,5-triphenyl-1H-imidazol-2-yl)phenyl)benzenamine (NTPB) and N-phenyl-N-(4-(1-phenyl-1H-phenanthro[9,10-d]imidazol-2-yl)phenyl)benzenamine (NPPB), that exhibited light induced reversible fluorescence switching via conformational change from a twisted molecular structure to more planar. NTPB and NPPB in CHCl3 showed red shift of absorption and fluorescence upon UV light irradiation whereas white light exposure reversed both absorption as well as fluorescence. The role of the TPA-imidazole twisted molecular structure in photoswitching was established based on structure property, computational and photophysical studies. The isobestic point observed in time dependent fluorescence change under UV light irradiation clearly demonstrated the presence of two different conformational isomers. Interestingly, polymorphism and torsion angle (τ) dependent fluorescence of NTPB and NPPB in the solid state also supported the role of the twisted molecular structure of TPA-imidazole in fluorescence switching/tuning. Interestingly, NTPB showed fluorescence photoswitching in the solid state also whereas rigid phenanthrene based NPPB did not show fluorescence photoswitching. Thus the present studies provide structural insight for designing a new type of fluorescent organic molecular photoswitches based on conformational modulation that could be of potential interest in optoelectronic devices.

In vitro toxicoproteomic analysis of A549 human lung epithelial cells exposed to urban air particulate matter and its water-soluble and insoluble fractions.

BACKGROUND: Toxicity of airborne particulate matter (PM) is difficult to assess because PM composition is complex and variable due to source contribution and atmospheric transformation. In this study, we used an in vitro toxicoproteomic approach to identify the toxicity mechanisms associated with different subfractions of Ottawa urban dust (EHC-93). METHODS: A549 human lung epithelial cells were exposed to 0, 60, 140 and 200 µg/cm2 doses of EHC-93 (total), its insoluble and soluble fractions for 24 h. Multiple cytotoxicity assays and proteomic analyses were used to assess particle toxicity in the exposed cells. RESULTS: The cytotoxicity data based on cellular ATP, BrdU incorporation and LDH leakage indicated that the insoluble, but not the soluble, fraction is responsible for the toxicity of EHC-93 in A549 cells. Two-dimensional gel electrophoresis results revealed that the expressions of 206 protein spots were significantly altered after particle exposures, where 154 were identified by MALDI-TOF-TOF-MS/MS. The results from cytotoxicity assays and proteomic analyses converged to a similar finding that the effects of the total and insoluble fraction may be alike, but their effects were distinguishable, and their effects were significantly different from the soluble fraction. Furthermore, the toxic potency of EHC-93 total is not equal to the sum of its insoluble and soluble fractions, implying inter-component interactions between insoluble and soluble materials resulting in synergistic or antagonistic cytotoxic effects. Pathway analysis based on the low toxicity dose (60 µg/cm2) indicated that the two subfractions can alter the expression of those proteins involved in pathways including cell death, cell proliferation and inflammatory response in a distinguishable manner. For example, the insoluble and soluble fractions differentially affected the secretion of pro-inflammatory cytokines such as MCP-1 and IL-8 and distinctly altered the expression of those proteins (e.g., TREM1, PDIA3 and ENO1) involved in an inflammatory response pathway in A549 cells. CONCLUSIONS: This study demonstrated the impact of different fractions of urban air particles constituted of various chemical species on different mechanistic pathways and thus on cytotoxicity effects. In vitro toxicoproteomics can be a valuable tool in mapping these differences in air pollutant exposure-related toxicity mechanisms.

Responses of A549 human lung epithelial cells to cristobalite and α-quartz exposures assessed by toxicoproteomics and gene expression analysis.

In this study, we used cytotoxicity assays, proteomic and gene expression analyses to examine the difference in response of A549 cells to two silica particles that differ in physical properties, namely cristobalite (CR) and α-quartz (Min-U-Sil 5, MI). Cytotoxicity assays such as lactate dehydrogenase release, 5-bromo-2'-deoxyuridine incorporation and cellular ATP showed that both silica particles could cause cell death, decreased cell proliferation and metabolism in the A549 human lung epithelial cells. While cytotoxicity assays revealed little difference between CR and MI exposures, proteomic and gene expression analyses unveiled both similar and unique molecular changes in A549 cells. For instance, two-dimensional gel electrophoresis data indicated that the expression of proteins in the cell death (e.g., ALDH1A1, HTRA2 and PRDX6) and cell proliferation (e.g., FSCN1, HNRNPAB and PGK1) pathways were significantly different between the two silica particles. Reverse transcription-polymerase chain reaction data provided additional evidence supporting the proteomic findings. Preliminary assessment of the physical differences between CR and MI suggested that the extent of surface interaction between particles and cells could explain some of the observed biological effects. However, the differential dose-response curves for some other genes and proteins suggest that other physical attributes of particulate matter can also contribute to particulate matter-related cellular toxicity. Our results demonstrated that toxicoproteomic and gene expression analyses are sensitive in distinguishing subtle toxicity differences associated with silica particles of varying physical properties compared to traditional cytotoxicity endpoints. Copyright © 2016 Her Majesty the Queen in Right of Canada. Journal of Applied Toxicology published by John Wiley & Sons, Ltd.

Structural basis for competitive inhibition of 3,4-dihydroxy-2-butanone-4-phosphate synthase from Vibrio cholerae.

The riboflavin biosynthesis pathway has been shown to be essential in many pathogens and is absent in humans. Therefore, enzymes involved in riboflavin synthesis are considered as potential antibacterial drug targets. The enzyme 3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) catalyzes one of the two committed steps in the riboflavin pathway and converts d-ribulose 5-phosphate (Ru5P) to l-3,4-dihydroxy-2-butanone 4-phosphate and formate. Moreover, DHBPS is shown to be indispensable for Mycobacterium, Salmonella, and Helicobacter species. Despite the essentiality of this enzyme in bacteria, no inhibitor has been identified hitherto. Here, we describe kinetic and crystal structure characterization of DHBPS from Vibrio cholerae (vDHBPS) with a competitive inhibitor 4-phospho-d-erythronohydroxamic acid (4PEH) at 1.86-Å resolution. In addition, we also report the structural characterization of vDHBPS in its apo form and in complex with its substrate and substrate plus metal ions at 1.96-, 1.59-, and 2.04-Å resolution, respectively. Comparison of these crystal structures suggests that 4PEH inhibits the catalytic activity of DHBPS as it is unable to form a proposed intermediate that is crucial for DHBPS activity. Furthermore, vDHBPS structures complexed with substrate and metal ions reveal that, unlike Candida albicans, binding of substrate to vDHBPS induces a conformational change from an open to closed conformation. Interestingly, the position of second metal ion, which is different from that of Methanococcus jannaschii, strongly supports an active role in the catalytic mechanism. Thus, the kinetic and structural characterization of vDHBPS reveals the molecular mechanism of inhibition shown by 4PEH and that it can be explored further for designing novel antibiotics.

Infant birth weight and third trimester maternal plasma markers of vascular integrity: the MIREC study.

BACKGROUND: There is paucity of information on mechanisms constituting adverse birth outcomes. We assessed here the relationship between vascular integrity and adverse birth effects. METHODS AND RESULTS: Third trimester maternal plasma (n = 144) from the Maternal-Infant Research on Environmental Chemicals Study (MIREC) was analysed for vascular, inflammatory and oxidative stress markers by HPLC-fluorescence, protein array and EIA method. Analysis of the <25th and >75th percentile birth weight subgroups revealed markers associated with birth weight (ETs, MMP-9, VEGF, and 8-isoPGF-2α) and gestational age (ET-1, MMP-2, and VEGF). CONCLUSIONS: Mechanistic insights into adverse birth outcome pathways can be achieved by integrating information on multiple biomarkers, physiology using systems biology approach.

Development of an integrated approach for comparison of in vitro and in vivo responses to particulate matter.

BACKGROUND: Association of particulate matter with adverse health effects has been established in epidemiological studies and animal experiments. Epidemiological studies are difficult to undertake while animal studies are impractical for high-throughput toxicity testing. The ease and rapidity of in vitro tests emphasizes their potential for use in risk assessment of chemicals and particles. We examined the association between in vitro and in vivo responses to ambient particles, to determine the potential of cell-based assays as standalone toxicity screening tools. METHODS: Assays of cytotoxicity and key inflammatory mediators were applied to determine the in vitro biological potency of a panel of urban and mineral particles in J774A.1 macrophages and A549 lung epithelial cells. The particles were also screened for the presence of AhR agonists using the Ah receptor-dependent gene induction assay and for endotoxin using the Limulus amebocyte lysate assay. A subset of the particles with a contrasting in vitro toxicity profile was delivered intratracheally in BALB/c mice to assess their in vivo biological potency. Results from various bioassays were combined within the in vitro and in vivo models. The combined potency measures were examined for associations. RESULTS: Overall, J774A.1 cells were more sensitive to particle effects than A549 cells. Whereas the combined cytotoxicity estimates were highly correlated between the two cell lines, the combined in vitro inflammatory potency estimates were not, emphasizing functional differences of the two cell types. Secretion of inflammatory markers by J774A.1 cells was correlated with AhR ligand binding profile and endotoxin levels of particles. Particle instillation led to an acute toxicity response in BALB/c mice, with neutrophilia and release of inflammatory mediators. While the combined toxicity estimates were not correlated between in vitro and in vivo models, the combined inflammatory and integrated potency estimates (toxicity and inflammation) approached the threshold for significance (p = 0.052) in a correlation within in vitro and in vivo models, with a ranking of fine particle (DWR1), minerals (TiO2, CRI) and coarse particles (SRM-, EHC-type) from low to high potency. CONCLUSION: Integration of in vitro endpoints shows promise in determining adverse outcomes of particle exposures in vivo. The devised data reduction and computational approach will prove useful in the development of models for assessment of hazard potential of particles; however, distinct models may be needed for particles of different type, such as urban particles vs. mineral particles, nanomaterials.

Contrasting biological potency of particulate matter collected at sites impacted by distinct industrial sources.

BACKGROUND: Industrial sources contribute a significant proportion of anthropogenic particulate matter (PM) emissions, producing particles of varying composition that may differentially impact health. This study investigated the in vitro toxicity of ambient PM collected near industrial sites in relation to particle size and composition. METHODS: Size-fractionated particles (ultrafine, PM0.1-2.5, PM2.5-10, PM>10) were collected in the vicinity of steel, copper, aluminium, and petrochemical industrial sites. Human lung epithelial-like A549 and murine macrophage-like J774A.1 cells were exposed for 24 h to particle suspensions (0, 30, 100, 300 µg/cm2). Particle potency was assessed using cytotoxic (resazurin reduction, lactate dehydrogenase (LDH) release) and inflammatory (cytokine release) assays, and regressed against composition (metals, polycyclic aromatic hydrocarbons (PAHs), endotoxin). RESULTS: Coarse (PM2.5-10, PM>10) particle fractions were composed primarily of iron and aluminium; in contrast, ultrafine and fine (PM0.1-2.5) fractions displayed considerable variability in metal composition (especially water-soluble metals) across collection sites consistent with source contributions. Semi-volatile and PM-associated PAHs were enriched in the fine and coarse fractions collected near metal industry. Cell responses to exposure at equivalent mass concentrations displayed striking differences among sites (SITE x SIZE and SITE x DOSE interactions, p < 0.05), suggesting that particle composition, in addition to size, impacted particle toxicity. While both J774A.1 and A549 cells exhibited clear particle size-dependent effects, site-dependent differences were more pronounced in J774A.1 cells, suggesting greater sensitivity to particle composition. Plotting particle potency according to cytotoxic and inflammatory response grouped particles by size and site, and showed that particles of similar composition tended to cluster together. Cytotoxic effects in J774A.1 cells correlated with metal and PAH content, while inflammatory responses were associated primarily with endotoxin content in coarse particles. CONCLUSIONS: Industrial sources produce particulate emissions with varying chemical composition that differ in their in vitro potency in relation to particle size and the levels of specific constituents.

Synthetic polyubiquitinated α-Synuclein reveals important insights into the roles of the ubiquitin chain in regulating its pathophysiology.

Ubiquitination regulates, via different modes of modifications, a variety of biological processes, and aberrations in the process have been implicated in the pathogenesis of several neurodegenerative diseases. However, our ability to dissect the pathophysiological relevance of the ubiquitination code has been hampered due to the lack of methods that allow site-specific introduction of ubiquitin (Ub) chains to a specific substrate. Here, we describe chemical and semisynthetic strategies for site-specific incorporation of K48-linked di- or tetra-Ub chains onto the side chain of Lys12 of α-Synuclein (α-Syn). These advances provided unique opportunities to elucidate the role of ubiquitination and Ub chain length in regulating α-Syn stability, aggregation, phosphorylation, and clearance. In addition, we investigated the cross-talk between phosphorylation and ubiquitination, the two most common α-Syn pathological modifications identified within Lewy bodies and Parkinson disease. Our results suggest that α-Syn functions under complex regulatory mechanisms involving cross-talk among different posttranslational modifications.

Structural and biochemical characterization of GTP cyclohydrolase II from Helicobacter pylori reveals its redox dependent catalytic activity.

GTP cyclohydrolase II (GCHII), catalyzes the conversion of GTP to 2,5-diamino-6-ß-ribosyl-4(3H)-pyrimidinone-5'-phosphate and has been shown to be essential for pathogens. Here we describe the biochemical, kinetic and structural characterization of GCHII from Helicobacter pylori (hGCHII). The crystal structure of hGCHII, unlike other GCHII structures, revealed that cysteines at the active site existed in oxidized state forming two disulfide bonds and lacked Zn(2+) that was shown to be indispensable for catalytic activity in other species. However, incubation of hGCHII with hydrogen peroxide, an oxidizing agent, followed by PAR-assay showed that Zn(2+) was intrinsically present, indicating that all cysteines at the catalytic site remained in reduced state. Moreover, site directed mutagenesis of catalytic site cysteines revealed that only three, out of four cysteines were essential for hGCHII activity. These results, though, indicated that hGCHII crystallized in oxidized form, the expulsion of Zn(2+) upon oxidation of catalytic cysteines revealed its ability to act in response to the redox environment. Exploring further, incubation of hGCHII with reversible thiol modifying agent S-methyl-methane-thiosulfonate resulted in loss of GCHII activity due to oxidation of its cysteine residues as revealed by mass spectrometry studies. However, addition of reducing agent DTT partially restored the hGCHII catalytic activity. Taken together, these results demonstrate that hGCHII can regulate its catalytic activity depending on the redox environment, a function hitherto unknown for GCHII.

Cytotoxic and inflammatory potential of size-fractionated particulate matter collected repeatedly within a small urban area.

BACKGROUND: Exposure to coarse, fine, and ultrafine particles is associated with adverse population health impacts. We investigated whether size-fractionated particles collected repeatedly in the vicinity of industrial (steel mills and associated coking operations, wastewater treatment), high traffic, and residential areas display systematic differences in biological potency. METHODS: Particulate matter (PM<0.1, PM0.1-0.5, PM0.5-2.5, PM2.5-10, PM>10) samples collected at sites within Windsor, Ontario, were screened for biological potency in human A549 lung epithelial and murine J774A.1 macrophage-like cells using cytotoxicity bioassays (cellular ATP, resazurin reduction, lactate dehydrogenase (LDH) release), cytokine production, and transcript profiles. Potency was determined from the slope of each dose-effect relationship. RESULTS: Cytotoxic potency varied across size fractions and within a fraction across sites and sampling periods, suggesting that particle composition, in addition to size and mass, affected particle toxicity. While ATP and LDH profiles showed some similarity, resazurin reduction (a measure of metabolic activity) exhibited a unique pattern of response, indicating that the cytotoxicity assays were sensitive to distinct particle characteristics. Chemical speciation varied in relation to prevailing winds, consistent with enrichment of source emissions (e.g. higher metal and polycyclic aromatic hydrocarbon content downwind of the industrial site). Notwithstanding this variability, site-dependent differences in particle toxicity were evident, including greater potency of coarse fractions at the industrial site and of ultrafine particles at the traffic site (Site × Size interactions, p < 0.05). Regression of potency against particle constituents revealed correlations between resazurin reduction, induction of metal-responsive genes, and metal content, which were particularly strong for the coarse fraction, and between cytokine release and endotoxin, suggesting that these factors were important drivers of biological effects that explain, at least in part, the contrasting potencies of particles compared on an equivalent mass basis. CONCLUSIONS: The data show that 1) particle potency and composition can exhibit significant temporal variation in relation to source contributions; 2) sources may differentially impact the potency of specific size fractions; and 3) particle constituents, notably metals and endotoxin, may elicit distinct biological responses. Together, the data are consistent with the notion that sources and composition, in addition to size and mass concentration, are relevant to particle toxicity.

Identification of crucial amino acids of bacterial Peptide deformylases affecting enzymatic activity in response to oxidative stress.

Peptide deformylase (PDF) is an essential bacterial metalloprotease involved in deformylation of N-formyl group from nascent polypeptide chains during protein synthesis. Iron-containing variants of this enzyme from Salmonella enterica serovar Typhimurium (sPDF) and Mycobacterium tuberculosis (mPDF), although inhibited by oxidizing agents like H2O2, exhibited strikingly different 50% inhibitory concentrations (IC50s) that ranged from nanomolar (sPDF) to millimolar (mPDF) levels. Furthermore, the metal dissociation rate was higher in sPDF than mPDF. We hypothesized that a restriction in entry of environmental oxygen or oxidizing agents into the active site of mPDF might be the cause for such discrepancies between two enzymes. Since the active-site residues of the two proteins are similar, we evaluated the role of the oxidation-prone noncatalytic residue(s) in the process. Amino acid sequence analysis revealed that Cys-130 of sPDF corresponds to Met-145 of mPDF and that they are away from the active sites. Swapping methionine with cysteine in mPDF, the M145C protein displayed a drastic decrease in the IC50 for H2O2 and an increased metal dissociation rate compared to the wild type. Matrix-assisted laser desorption ionization (MALDI) analysis of a trypsin-digested fragment containing Cys-145 of the M145C protein also indicated its increased susceptibility to oxidation. To incorporate residues identical to those of mPDF, we created a double mutant of sPDF (C130M-V63C) that showed increased IC50 for H2O2 compared to the wild type. Interestingly, the oxidation state of cysteines in C130M-V63C was unaffected during H2O2 treatment. Taken together, our results unambiguously established the critical role of noncatalytic cysteine/methionine for enzymatic sensitivity to H2O2 and, thus, for conferring behavioral distinction of bacterial PDFs under oxidative stress conditions.

Biochemical and structural characterization reveals Rv3400 codes for ß-phosphoglucomutase in Mycobacterium tuberculosis.

Mycobacterium tuberculosis (Mtb) adapt to various host environments and utilize a variety of sugars and lipids as carbon sources. Among these sugars, maltose and trehalose, also play crucial role in bacterial physiology and virulence. However, some key enzymes involved in trehalose and maltose metabolism in Mtb are not yet known. Here we structurally and functionally characterized a conserved hypothetical gene Rv3400. We determined the crystal structure of Rv3400 at 1.7 Å resolution. The crystal structure revealed that Rv3400 adopts Rossmann fold and shares high structural similarity with haloacid dehalogenase family of proteins. Our comparative structural analysis suggested that Rv3400 could perform either phosphatase or pyrophosphatase or ß-phosphoglucomutase (ß-PGM) activity. Using biochemical studies, we further confirmed that Rv3400 performs ß-PGM activity and hence, Rv3400 encodes for ß-PGM in Mtb. Our data also confirm that Mtb ß-PGM is a metal dependent enzyme having broad specificity for divalent metal ions. ß-PGM converts ß-D-glucose-1-phosphate to ß-D-glucose-6-phosphate which is required for the generation of ATP and NADPH through glycolysis and pentose phosphate pathway, respectively. Using site directed mutagenesis followed by biochemical studies, we show that two Asp residues in the highly conserved DxD motif, D29 and D31, are crucial for enzyme activity. While D29A, D31A, D29E, D31E and D29N mutants lost complete activity, D31N mutant retained about 30% activity. This study further helps in understanding the role of ß-PGM in the physiology of Mtb.