Elemental Analysis ofMycobacterium avium-,Mycobacterium tuberculosis-, andMycobacterium smegmatis-Containing Phagosomes Indicates Pathogen-Induced Microenvironments within the Host Cell’s Endosomal System

Single-cell elemental analysis of bacteria: quantitative analysis of polyphosphates in Mycobacterium tuberculosis

More than 1.8 million people die annually from infection with Mycobacterium tuberculosis, the causative agent of tuberculosis. The ability of M. tuberculosis to obtain and distribute micronutrients, including biometals, is known to play a role in its intracellular survival and virulence within a host. Techniques to detect elemental distributions within M. tuberculosis cells have previously been limited to bulk detection methods or low-resolution analyses. Here, we present a method for determining the elemental distribution within M. tuberculosis on a single-cell level, at high (individual nanometer) resolution, using scanning transmission electron microscopy (STEM) in concert with energy-dispersive X-ray spectroscopy (EDS). Results revealed the presence of large polyphosphate granules in all strains of Mycobacteria tested. These persisted even through starvation conditions, and might play a role connected to elemental homeostasis in M. tuberculosis. Associated with the polyphosphate granules were micronutrients such as calcium and magnesium. In addition, we expanded the technique beyond Mycobacteria to show that STEM and EDS could be used as a simple screen to detect the presence or absence of concentrated elements on a single-cell level within all six other bacterial types tested, with minimal processing to the bacteria. Overall, we believe that this technique represents a first step in developing a better understanding of the role that components of the intracellular milieu, including polyphosphates and biometals, play in the pathogenesis of M. tuberculosis, with potential future applications for in vivo analysis.

Role in metal homeostasis of CtpD, a Co²⁺ transporting P(1B4)-ATPase of Mycobacterium smegmatis

Genetic studies in the tuberculosis mouse model have suggested that mycobacterial metal efflux systems, such as the P(1B4)-ATPase CtpD, are important for pathogenesis. The specificity for substrate metals largely determines the function of these ATPases; however, various substrates have been reported for bacterial and plant P(1B4)-ATPases leaving their function uncertain. Here we describe the functional role of the CtpD protein of Mycobacterium smegmatis. An M. smegmatis mutant strain lacking the ctpD gene was hypersensitive to Co²⁺ and Ni²⁺ and accumulated these metals in the cytoplasm. ctpD transcription was induced by both Co²⁺ and superoxide stress. Biochemical characterization of heterologously expressed, affinity-purified CtpD showed that this ATPase is activated by Co²⁺, Ni²⁺ and to a lesser extend Zn²⁺ (20% of maximum activity). The protein was also able to bind one Co²⁺, Ni²⁺ or Zn²⁺ to its transmembrane transport site. These observations indicate that CtpD is important for Co²⁺ and Ni²⁺ homeostasis in M. smegmatis, and that M. tuberculosis CtpD orthologue could be involved in metal detoxification and resisting cellular oxidative stress by modulating the intracellular concentration of these metals.

Interferon-inducible effector mechanisms in cell-autonomous immunity

Interferons (IFNs) induce the expression of hundreds of genes as part of an elaborate antimicrobial programme designed to combat infection in all nucleated cells - a process termed cell-autonomous immunity. As described in this Review, recent genomic and subgenomic analyses have begun to assign functional properties to novel IFN-inducible effector proteins that restrict bacteria, protozoa and viruses in different subcellular compartments and at different stages of the pathogen life cycle. Several newly described host defence factors also participate in canonical oxidative and autophagic pathways by spatially coordinating their activities to enhance microbial killing. Together, these IFN-induced effector networks help to confer vertebrate host resistance to a vast and complex microbial world.

Mycobacteria and the intraphagosomal environment: take it with a pinch of salt(s)!

Ancient protozoan phagocytes and modern professional phagocytes of metazoans, such as macrophages, employ evolutionarily conserved mechanisms to kill microbes. These mechanisms rely on microbial ingestion, followed by maturation of the phagocytic vacuole, or so-called phagosome. Phagosome maturation includes a series of fusion and fission events with the host cell endosomes and lysosomes, leading to a rapid increase of the degradative properties of the vacuole and to the destruction of the ingested microbe within a very hostile intracellular compartment, the phagolysosome. Historically, the mechanisms and weapons used by phagocytes to kill microbes have been separated into different classes. Phagosomal acidification, together with the production of reactive oxygen and nitrogen species, the selective manipulation of various ions in the phagosomal lumen, and finally the engagement of a battery of acidic hydrolases, are well-recognized players in this process. However, it is relatively recently that interconnections among these mechanisms have become apparent. In this review, we will focus on some emerging concepts about these interconnected aspects of the warfare at the host-pathogen interface, using mostly Mycobacterium tuberculosis as an example of intracellular pathogen. In particular, recent discoveries on the role of phagosomal ions and other chemicals in the control of pathogens, as well as mechanisms evolved by intracellular pathogens to circumvent or even exploit the weapons of the host cell will be discussed.

Staphylococcal response to oxidative stress

Staphylococci are a versatile genus of bacteria that are capable of causing acute and chronic infections in diverse host species. The success of staphylococci as pathogens is due in part to their ability to mitigate endogenous and exogenous oxidative and nitrosative stress. Endogenous oxidative stress is a consequence of life in an aerobic environment; whereas, exogenous oxidative and nitrosative stress are often due to the bacteria's interaction with host immune systems. To overcome the deleterious effects of oxidative and nitrosative stress, staphylococci have evolved protection, detoxification, and repair mechanisms that are controlled by a network of regulators. In this review, we summarize the cellular targets of oxidative stress, the mechanisms by which staphylococci sense oxidative stress and damage, oxidative stress protection and repair mechanisms, and regulation of the oxidative stress response. When possible, special attention is given to how the oxidative stress defense mechanisms help staphylococci control oxidative stress in the host.

Copper homeostasis at the host-pathogen interface

The trace element copper is indispensable for all aerobic life forms. Its ability to cycle between two oxidation states, Cu(1+) and Cu(2+), has been harnessed by a wide array of metalloenzymes that catalyze electron transfer reactions. The metabolic needs for copper are sustained by a complex series of transporters and carrier proteins that regulate its intracellular accumulation and distribution in both pathogenic microbes and their animal hosts. However, copper is also potentially toxic due in part to its ability to generate reactive oxygen species. Recent studies suggest that the macrophage phagosome accumulates copper during bacterial infection, which may constitute an important mechanism of killing. Bacterial countermeasures include the up-regulation of copper export and detoxification genes during infection, which studies suggest are important determinants of virulence. In this minireview, we summarize recent developments that suggest an emerging role for copper as an unexpected component in determining the outcome of host-pathogen interactions.

Resistance mechanisms of Mycobacterium tuberculosis against phagosomal copper overload

Mycobacterium tuberculosis is an important bacterial pathogen with an extremely slow growth rate, an unusual outer membrane of very low permeability and a cunning ability to survive inside the human host despite a potent immune response. A key trait of M. tuberculosis is to acquire essential nutrients while still preserving its natural resistance to toxic compounds. In this regard, copper homeostasis mechanisms are particularly interesting, because copper is an important element for bacterial growth, but copper overload is toxic. In M. tuberculosis at least two enzymes require copper as a cofactor: the Cu/Zn-superoxide dismutase SodC and the cytochrome c oxidase which is essential for growth in vitro. Mutants of M. tuberculosis lacking the copper metallothionein MymT, the efflux pump CtpV and the membrane protein MctB are more susceptible to copper indicating that these proteins are part of a multipronged system to balance intracellular copper levels. Recent evidence showed that part of copper toxicity is a reversible damage of Fe-S clusters of dehydratases and the displacement of other divalent cations such as zinc and manganese as cofactors in proteins. There is accumulating evidence that macrophages use copper to poison bacteria trapped inside phagosomes. Here, we review the rapidly increasing knowledge about copper homeostasis in M. tuberculosis and contrast those with similar mechanisms in Escherichia coli. These findings reveal an intricate interplay between the host which aims to overload the phagosome with copper and M. tuberculosis which utilizes several mechanisms to reduce the toxic effects of excess copper.

Global changes in gene expression by the opportunistic pathogen Burkholderia cenocepacia in response to internalization by murine macrophages

Background

Burkholderia cenocepacia is an opportunistic pathogen causing life-threatening infections in patients with cystic fibrosis. The bacterium survives within macrophages by interfering with endocytic trafficking and delaying the maturation of the B. cenocepacia-containing phagosome. We hypothesize that B. cenocepacia undergoes changes in gene expression after internalization by macrophages, inducing genes involved in intracellular survival and host adaptation.

Results

We examined gene expression by intracellular B. cenocepacia using selective capture of transcribed sequences (SCOTS) combined with microarray analysis. We identified 767 genes with significantly different levels of expression by intracellular bacteria, of which 330 showed increased expression and 437 showed decreased expression. Affected genes represented all aspects of cellular life including information storage and processing, cellular processes and signaling, and metabolism. In general, intracellular gene expression demonstrated a pattern of environmental sensing, bacterial response, and metabolic adaptation to the phagosomal environment. Deletion of various SCOTS-identified genes affected bacterial entry into macrophages and intracellular replication. We also show that intracellular B. cenocepacia is cytotoxic towards the macrophage host, and capable of spread to neighboring cells, a role dependent on SCOTS-identified genes. In particular, genes involved in bacterial motility, cobalamin biosynthesis, the type VI secretion system, and membrane modification contributed greatly to macrophage entry and subsequent intracellular behavior of B. cenocepacia.

Conclusions

B. cenocepacia enters macrophages, adapts to the phagosomal environment, replicates within a modified phagosome, and exhibits cytotoxicity towards the host cells. The analysis of the transcriptomic response of intracellular B. cenocepacia reveals that metabolic adaptation to a new niche plays a major role in the survival of B. cenocepacia in macrophages. This adaptive response does not require the expression of any specific virulence-associated factor, which is consistent with the opportunistic nature of this microorganism. Further investigation into the remaining SCOTS-identified genes will provide a more complete picture of the adaptive response of B. cenocepacia to the host cell environment.

Metallobiology of host-pathogen interactions: an intoxicating new insight

Iron, zinc and copper, among others, are transition metals with multiple biological roles that make them essential elements for life. Beyond the strict requirement of transition metals by the vertebrate immune system for its proper functioning, novel mechanisms involving direct metal intoxication of microorganisms are starting to be unveiled as important components of the immune system, in particular against Mycobacterium tuberculosis. In parallel, metal detoxification systems in bacteria have been recently characterized as crucial microbial virulence determinants. Here, we will focus on these exciting advancements implicating copper- and zinc-mediated microbial poisoning as a novel innate immune mechanism against microbial pathogens, shedding light on an emerging field in the metallobiology of host-pathogen interactions.

Mycobacterial p(1)-type ATPases mediate resistance to zinc poisoning in human macrophages

Mycobacterium tuberculosis thrives within macrophages by residing in phagosomes and preventing them from maturing and fusing with lysosomes. A parallel transcriptional survey of intracellular mycobacteria and their host macrophages revealed signatures of heavy metal poisoning. In particular, mycobacterial genes encoding heavy metal efflux P-type ATPases CtpC, CtpG, and CtpV, and host cell metallothioneins and zinc exporter ZnT1, were induced during infection. Consistent with this pattern of gene modulation, we observed a burst of free zinc inside macrophages, and intraphagosomal zinc accumulation within a few hours postinfection. Zinc exposure led to rapid CtpC induction, and ctpC deficiency caused zinc retention within the mycobacterial cytoplasm, leading to impaired intracellular growth of the bacilli. Thus, the use of P₁-type ATPases represents a M. tuberculosis strategy to neutralize the toxic effects of zinc in macrophages. We propose that heavy metal toxicity and its counteraction might represent yet another chapter in the host-microbe arms race.

The galvanizing of Mycobacterium tuberculosis: an antimicrobial mechanism

Evolving under constant threat from invading microbes, macrophages have acquired multiple means of killing bacteria. In this issue of Cell Host & Microbe, Botella and colleagues (Botella et al., 2011) describe a novel antimicrobial mechanism based on elevated levels of intraphagosomal Zn(2+) and the corresponding induction of bacterial genes to ameliorate this host-derived stress.

Toward a molecular understanding of metal transport by P(1B)-type ATPases

The P(1B) family of P-type ATPases couples the transport of cytoplasmic transition metals across biological membranes to the hydrolysis of ATP. These ubiquitous transporters function in maintaining cytoplasmic metal quotas and in the assembly of metalloproteins, and have been classified into subfamilies (P(1B-1)-P(1B-5)) on the basis of their transported substrates (Cu(+), Zn(2+), Cu(2+), and Co(2+)) and signature sequences in their transmembrane segments. In addition, each subgroup presents a characteristic membrane topology and specific regulatory cytoplasmic metal-binding domains. In recent years, significant major aspects of their transport mechanism have been described, including the stoichiometry of transport and the delivery of substrates to transport sites by metallochaperones. Toward understanding their structure, the metal coordination by transport sites has been characterized for Cu(+) and Zn(2+)-ATPases. In addition, atomic resolution structures have been determined, providing key insight into the elements that enable transition metal transport. Because the Cu(+)-transporting ATPases are found in humans and are linked to disease, this subfamily has been the focus of intense study. As a result, significant progress has been made toward understanding Cu(+)-ATPase function on the molecular level, using both the human proteins and the bacterial homologs, most notably the CopA proteins from Archaeoglobus fulgidus, Bacillus subtilis, and Thermotoga maritima. This chapter thus focuses on the mechanistic and structural information obtained by studying these latter Cu(+)-ATPases, with some consideration of how these aspects might differ for the other subfamilies of P(1B)-ATPases.

Paradoxical roles of alveolar macrophages in the host response to Cryptococcus neoformans

Cryptococcus neoformans (Cn) is a fungal pathogen that is a serious health threat to immunocompromised individuals. Upon environmental exposure, infectious fungal propagules are inhaled into the host's lungs. The anticryptococcal actions of alveolar macrophages (AM), the predominant host phagocyte of the innate immune system in the lungs, are fundamental in determining whether containment and clearance of the pathogen occurs by the development of an adapted immune response or whether infection is established and progresses to disease. However, the fungus is also capable of surviving the antimicrobial actions of AM and exploits these host phagocytes to establish infection and exacerbate disease. In addition, there is evidence suggesting that cryptococcosis may occur following reactivation of latent cryptococcal infection. Currently, the role of AM and the fungal factors contributing to latent cryptococcosis are unknown. This review examines the AM-Cn interaction and how it affects the development of pulmonary disease with a focus on host and pathogen factors enabling latency to occur.

Bacterial transition metal P(1B)-ATPases: transport mechanism and roles in virulence

P(1B)-type ATPases are polytopic membrane proteins that couple the hydrolysis of ATP to the efflux of cytoplasmic transition metals. This paper reviews recent progress in our understanding of the structure and function of these proteins in bacteria. These are members of the P-type superfamily of transport ATPases. Cu(+)-ATPases are the most frequently observed and best-characterized members of this group of transporters. However, bacterial genomes show diverse arrays of P(1B)-type ATPases with a range of substrates (Cu(+), Zn(2+), Co(2+)). Furthermore, because of the structural similarities among transitions metals, these proteins can also transport nonphysiological substrates (Cd(2+), Pb(2+), Au(+), Ag(+)). P(1B)-type ATPases have six or eight transmembrane segments (TM) with metal coordinating amino acids in three core TMs flanking the cytoplasmic domain responsible for ATP binding and hydrolysis. In addition, regulatory cytoplasmic metal binding domains are present in most P(1B)-type ATPases. Central to the transport mechanism is the binding of the uncomplexed metal to these proteins when cytoplasmic substrates are bound to chaperone and chelating molecules. Metal binding to regulatory sites is through a reversible metal exchange among chaperones and cytoplasmic metal binding domains. In contrast, the chaperone-mediated metal delivery to transport sites appears as a largely irreversible event. P(1B)-ATPases have two overarching physiological functions: to maintain cytoplasmic metal levels and to provide metals for the periplasmic assembly of metalloproteins. Recent studies have shown that both roles are critical for bacterial virulence, since P(1B)-ATPases appear key to overcome high phagosomal metal levels and are required for the assembly of periplasmic and secreted metalloproteins that are essential for survival in extreme oxidant environments.

Pharmacokinetic/pharmacodynamic-based treatment of disseminated Mycobacterium avium

Disseminated Mycobacterium avium complex (MAC) is treated with a macrolide and ethambutol. However, the kill rates are extremely slow so that therapy takes many months to years to achieve and even then more than 40% of patients are not completely cured. Recent studies have demonstrated that assays that detect extracellular MAC have a limited predictive value. Antibiotics kill at a much slower and more disappointing rate against bacilli within macrophages. Use of pharmacodynamic/pharmacokinetic models has resulted in design of new doses and dosing schedules for disseminated MAC, as well as new susceptibility breakpoints for ethambutol and moxifloxacin.

Mycobacterium tuberculosis NmtR harbors a nickel sensing site with parallels to Escherichia coli RcnR

Mycobacterium tuberculosis NmtR is a Ni(II)/Co(II)-sensing metalloregulatory protein from the extensively studied ArsR/SmtB family. Two Ni(II) ions bind to the NmtR dimer to form octahedral coordination complexes with the following stepwise binding affinities: K(Ni1) = (1.2 ± 0.1) × 10(10) M(-1), and K(Ni2) = (0.7 ± 0.4) × 10(10) M(-1) (pH 7.0). A glutamine scanning mutagenesis approach reveals that Asp91, His93, His104, and His107, all contained within the C-terminal α5 helix, and His3 as part of the conserved α-NH(2)-Gly2-His3-Gly4 motif at the N-terminus make significant contributions to the magnitude of K(Ni). In contrast, substitution of residues from the C-terminal region, His109, Asp114, and His116, previously implicated in Ni(II) binding and metalloregulation in cells, gives rise to wild-type K(Ni) and Ni(II)-dependent allosteric coupling free energies. Interestingly, deletion of residues 112-120 from the C-terminal region (Δ111 NmtR) reduces the Ni(II) binding stoichiometry to one per dimer and greatly reduces Ni(II) responsiveness. H3Q and Δ111 NmtRs also show clear perturbations in the rank order of metal responsiveness to Ni(II), Co(II), and Zn(II) that is distinct from that of wild-type NmtR. (15)N relaxation experiments with apo-NmtR reveal that both N-terminal (residues 2-14) and C- terminal (residues 110-120) regions are unstructured in solution, and this property likely dictates the metal specificity profile characteristic of the Ni(II) sensor NmtR relative to other ArsR family regulators.

Demand for Zn2+ in acid-secreting gastric mucosa and its requirement for intracellular Ca2+

BACKGROUND AND AIMS

Recent work has suggested that Zn(2+) plays a critical role in regulating acidity within the secretory compartments of isolated gastric glands. Here, we investigate the content, distribution and demand for Zn(2+) in gastric mucosa under baseline conditions and its regulation during secretory stimulation.

METHODS AND FINDINGS

Content and distribution of zinc were evaluated in sections of whole gastric mucosa using X-ray fluorescence microscopy. Significant stores of Zn(2+) were identified in neural elements of the muscularis, glandular areas enriched in parietal cells, and apical regions of the surface epithelium. In in vivo studies, extraction of the low abundance isotope, (70)Zn(2+), from the circulation was demonstrated in samples of mucosal tissue 24 hours or 72 hours after infusion (250 µg/kg). In in vitro studies, uptake of (70)Zn(2+) from media was demonstrated in isolated rabbit gastric glands following exposure to concentrations as low as 10 nM. In additional studies, demand of individual gastric parietal cells for Zn(2+) was monitored using the fluorescent zinc reporter, fluozin-3, by measuring increases in free intracellular concentrations of Zn(2+) {[Zn(2+)](i)} during exposure to standard extracellular concentrations of Zn(2+) (10 µM) for standard intervals of time. Under resting conditions, demand for extracellular Zn(2+) increased with exposure to secretagogues (forskolin, carbachol/histamine) and under conditions associated with increased intracellular Ca(2+) {[Ca(2+)](i)}. Uptake of Zn(2+) was abolished following removal of extracellular Ca(2+) or depletion of intracellular Ca(2+) stores, suggesting that demand for extracellular Zn(2+) increases and depends on influx of extracellular Ca(2+).

CONCLUSIONS

This study is the first to characterize the content and distribution of Zn(2+) in an organ of the gastrointestinal tract. Our findings offer the novel interpretation, that Ca(2+) integrates basolateral demand for Zn(2+) with stimulation of secretion of HCl into the lumen of the gastric gland. Similar connections may be detectable in other secretory cells and tissues.

The activity and cofactor preferences of N-acetyl-1-D-myo-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase (MshB) change depending on environmental conditions

Actinomycetes, such as Mycobacterium species, are Gram-positive bacteria that utilize the small molecule mycothiol (MSH) as their primary reducing agent. Consequently, the enzymes involved in MSH biosynthesis are targets for drug development. The metal-dependent enzyme N-acetyl-1-D-myo-inosityl-2-amino-2-deoxy-α-D-glucopyranoside deacetylase (MshB) catalyzes the hydrolysis of N-acetyl-1-D-myo-inosityl-2-amino-2-deoxy-α-D-glucopyranoside to form 1-D-myo-inosityl-2-amino-2-deoxy-α-D-glucopyranoside and acetate, the fourth overall step in MSH biosynthesis. Inhibitors of metalloenzymes typically contain a group that binds to the active site metal ion; thus, a comprehensive understanding of the native cofactor(s) of metalloenzymes is critical for the development of biologically effective inhibitors. Herein, we examined the effect of metal ions on the overall activity of MshB and probed the identity of the native cofactor. We found that the activity of MshB follows the trend Fe(2+) > Co(2+) > Zn(2+) > Mn(2+) and Ni(2+). Additionally, our results show that the identity of the cofactor bound to purified MshB is highly dependent on the purification conditions used (aerobic versus anaerobic), as well as the metal ion content of the medium during protein expression. MshB prefers Fe(2+) under anaerobic conditions regardless of the metal ion content of the medium and switches between Fe(2+) and Zn(2+) under aerobic conditions as the metal content of the medium is altered. These results indicate that the cofactor bound to MshB under biological conditions is dependent on environmental conditions, suggesting that MshB may be a cambialistic metallohydrolase that contains a dynamic cofactor. Consequently, biologically effective inhibitors will likely need to dually target Fe(2+)-MshB and Zn(2+)-MshB.

Mimicry of the pathogenic mycobacterium vacuole in vitro elicits the bacterial intracellular phenotype, including early-onset macrophage death

Mycobacterium avium complex (MAC) within macrophages undergoes a phenotype change that allows for more efficient entry into surrounding host cells. We hypothesized that, by developing an in vitro system resembling the intravacuolar environment, one could generate insights into the mycobacterial intracellular phenotype. MAC was incubated in "elemental mixtures" that reproduce metal concentrations and pH in the vacuoles at different time points and then used to infect fresh macrophages. Incubation of MAC with the mixture corresponding to the vacuole environment 24 h postinfection infected macrophages at a significantly higher rate than bacteria that were incubated in Middlebrook 7H9 broth. Uptake occurred by macropinocytosis, similar to the uptake of bacteria passed through macrophages. Genes reported to be upregulated in intracellular bacteria, such as Mav1365, Mav2409, Mav4487, and Mav0996, were upregulated in MAC incubated in the 24-h elemental mixture. Like MAC obtained from macrophages, the vacuoles of bacteria from the 24-h elemental mixture were more likely to contain lysosome-associated membrane protein 1 (LAMP-1). A stepwise reduction scheme of the 24-h elemental mixture indicated that incubation in physiologically relevant concentrations of potassium chloride, calcium chloride, and manganese chloride was sufficient to induce characteristics of the intracellular phenotype. It was demonstrated that bacteria harboring the intracellular phenotype induced early-onset macrophage death more efficiently than bacteria grown in broth. This new trace elemental mixture mimicking the condition of the vacuole at different time points has the potential to become an effective laboratory tool for the study of the MAC and Mycobacterium tuberculosis disease process, increasing the understanding of the interaction with macrophages.

Phosphorylation of Mycobacterium tuberculosis Ser/Thr phosphatase by PknA and PknB

Background

The integrated functions of 11 Ser/Thr protein kinases (STPKs) and one phosphatase manipulate the phosphorylation levels of critical proteins in Mycobacterium tuberculosis. In this study, we show that the lone Ser/Thr phosphatase (PstP) is regulated through phosphorylation by STPKs.

Principal Findings

PstP is phosphorylated by PknA and PknB and phosphorylation is influenced by the presence of Zn²⁺-ions and inorganic phosphate (Pi). PstP is differentially phosphorylated on the cytosolic domain with Thr¹³⁷, Thr¹⁴¹, Thr¹⁷⁴ and Thr²⁹⁰ being the target residues of PknB while Thr¹³⁷ and Thr¹⁷⁴ are phosphorylated by PknA. The Mn²⁺-ion binding residues Asp³⁸ and Asp²²⁹ are critical for the optimal activity of PstP and substitution of these residues affects its phosphorylation status. Native PstP and its phosphatase deficient mutant PstP_c^D38G are phosphorylated by PknA and PknB in E. coli and addition of Zn²⁺/Pi in the culture conditions affect the phosphorylation level of PstP. Interestingly, the phosphorylated phosphatase is more active than its unphosphorylated equivalent.

Conclusions and Significance

This study establishes the novel mechanisms for regulation of mycobacterial Ser/Thr phosphatase. The results indicate that STPKs and PstP may regulate the signaling through mutually dependent mechanisms. Consequently, PstP phosphorylation may play a critical role in regulating its own activity. Since, the equilibrium between phosphorylated and non-phosphorylated states of mycobacterial proteins is still unexplained, understanding the regulation of PstP may help in deciphering the signal transduction pathways mediated by STPKs and the reversibility of the phenomena.

Nitric oxide-mediated intracellular growth restriction of pathogenic Rhodococcus equi can be prevented by iron

Rhodococcus equi is an intracellular pathogen which causes pneumonia in young horses and in immunocompromised humans. R. equi arrests phagosome maturation in macrophages at a prephagolysosome stage and grows inside a privileged compartment. Here, we show that, in murine macrophages activated with gamma interferon and lipopolysaccharide, R. equi does not multiply but stays viable for at least 24 h. Whereas infection control of other intracellular pathogens by activated macrophages is executed by enhanced phagosome acidification or phagolysosome formation, by autophagy or by the interferon-inducible GTPase Irgm1, none of these mechanisms seems to control R. equi infection. Growth control by macrophage activation is fully mimicked by treatment of resting macrophages with nitric oxide donors, and inhibition of bacterial multiplication by either activation or nitric oxide donors is annihilated by cotreatment of infected macrophages with ferrous sulfate. Transcriptional analysis of the R. equi iron-regulated gene iupT demonstrates that intracellular R. equi encounters iron stress in activated, but not in resting, macrophages and that this stress is relieved by extracellular addition of ferrous sulfate. Our results suggest that nitric oxide is central to the restriction of bacterial access to iron in activated macrophages.

CtpV: a putative copper exporter required for full virulence of Mycobacterium tuberculosis

Copper is a required micronutrient that is also toxic at excess concentrations. Currently, little is known about the role of copper in interactions between bacterial pathogens and their human hosts. In this study, we elucidate a mechanism for copper homeostasis in the human pathogen Mycobacterium tuberculosis via characterization of a putative copper exporter, CtpV. CtpV was shown to be required by M. tuberculosis to maintain resistance to copper toxicity. Furthermore, the deletion of ctpV resulted in a 98-gene transcriptional response, which elucidates the increased stress experienced by the bacteria in the absence of this detoxification mechanism. Interestingly, although the ΔctpV mutant survives close to the wild-type levels in both murine and guinea pig models of tuberculosis, animals infected with the ΔctpV mutant displayed decreased lung damage, and mutant-infected mice had a reduced immune response to the bacteria as well as a significant increase in survival time relative to mice infected with wild-type M. tuberculosis. Overall, our study provides the first evidence for a connection between bacterial copper response and the virulence of M. tuberculosis, supporting the hypothesis that copper response could be important to intracellular pathogens, in general.

Mycobacterium tuberculosis mtrA merodiploid strains with point mutations in the signal-receiving domain of MtrA exhibit growth defects in nutrient broth

The genetic and biochemical aspects of the essential Mycobacteriumtuberculosis MtrAB two-component regulatory signal transduction (2CRS) system have not been extensively investigated. We show by bacterial two-hybrid assay that the response regulator (RR) MtrA and the sensor kinase MtrB interact. We further demonstrate that divalent metal ions [Mg²+, Ca²+ or both] promote MtrB kinase autophosphorylation activity, but only Mg²+ promotes phosphotransfer to MtrA. Replacement of the conserved aspartic acid residues at positions 13 and 56 with alanine (D13A), glutamine (D56E) or asparagine (D56N) prevented MtrA phosphorylation, indicating that these residues are important for phosphorylation. The MtrA(D56E) and MtrA(D13A) proteins bound to the promoter of fbpB, the gene encoding antigen 85B protein, efficiently in the absence of phosphorylation, whereas MtrA(D56N) did not. We also show that M.tuberculosismtrA merodiploids overproducing MtrA(D13A), unlike cells overproducing wild-type MtrA, grow poorly in nutrient broth and show reduced expression of fbpB. These latter findings are reminiscent of a phenotype associated with MtrA overproduction during intramacrophage growth. Our results suggest that MtrA(D13A) behaves like a constitutively active response regulator and that further characterization of mtrA merodiploid strains will provide valuable clues to the MtrAB system.

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

A human alveolar macrophage genome-scale metabolic reconstruction was reconstructed from tailoring a global human metabolic network, Recon 1, by using computational algorithms and manual curation.

A genome-scale host–pathogen network of the human alveolar macrophage and Mycobacterium tuberculosis is presented. This involved integrating two genome-scale network reconstructions.

The reaction activity and gene essentiality predictions of the host–pathogen model represent a more accurate depiction of infection.

Integration of high-throughput data into a host-pathogen model followed by systems analysis was performed in order to elucidate major metabolic differences under different types of M. tuberculosis infection.

Mycobacterium tuberculosis (M. tb) is an insidious and highly persistent pathogen that affects one-third of the world's population (WHO, 2009). Metabolism is foundational to M. tb's infection ability and the ensuing host–pathogen interactions. In addition, M. tb has a heterogeneous clinical presentation and can infect virtually every tissue. Depending on the location of the infection, different metabolic pathways are active and inactive in both the host and pathogen cells. In this study, we sought to model the host–pathogen interactions of the human alveolar macrophage and M. tb as well as detail the metabolic differences in specific infection types using genome-scale metabolic reconstructions (Figure 4A).

Genome-scale metabolic reconstructions are knowledge bases of all known metabolic reactions of a given organism. Reconstructions have been shown to elucidate the mechanistic genotype-to-phenotype relationship through the integration of high-throughput and physiological data (Oberhardt et al, 2009). Genome-scale reconstructions are converted into mathematical models under the constraints-based reconstruction and analysis (COBRA) platform (Becker et al, 2007). COBRA models use network stoichiometry and steady-state mass balances to define a solution space of potential flux states that a network can take. Thus, the COBRA approach does not require kinetic parameters.

Recently, the global human metabolic network, Recon 1, has been reconstructed (Duarte et al, 2007). To understand the metabolic host–pathogen integrations of M. tb with its human host, we first tailored the global human metabolic network into a cell-specific metabolic reconstruction of the human alveolar macrophage. This was carried out using established computational algorithms (Becker and Palsson, 2008; Shlomi et al, 2008) and manual curation to confirm the included and excluded reactions. The human alveolar macrophage reconstruction, iAB-AMØ-1410, accounts for 1410 genes, 3012 intracellular reactions, and 2572 metabolites (Figure 4C). iAB-AMØ-1410 was able to accurately predict maximum ATP and NO production rates obtained from experimental data (Griscavage et al, 1993; Newsholme et al, 1999).

The second step to studying host–pathogen interactions was integration of the human alveolar macrophage reconstruction with an existing genome-scale metabolic model of M. tb, iNJ661 (Jamshidi and Palsson, 2007). Interfacial constraints were set to create a phagosomal environment that was hypoxic, nitrosative, rich in fatty acids, and poor in carbohydrates. From the onset, it was apparent that some oxygen (<15% of in vitro uptake) was required for proper simulations. In addition, algorithmic tailoring of the M. tb biomass objective function was performed to better represent an infectious state. The integrated host–pathogen metabolic reconstruction was dubbed iAB-AMØ-1410-Mt-661.

Analysis of the integrated host–pathogen metabolic reconstruction resulted in three main findings. First, by setting interfacial constraints and tailoring the biomass objective function, the solution space better represents an infectious state. Without adding artificial constraints to the host portion of the integrated model, the iAB-AMØ-1410 solution space is greatly reduced (Figure 4B). Macrophage glycolysis and nitric oxide production are up-regulated and macrophage ATP production, nucleotide synthesis, and amino-acid metabolism are suppressed. In addition, M. tb glycolysis is suppressed and isocitrate lyase is up-regulated for generation of acetyl-CoA. Fatty acid oxidation pathways and production of mycolic acids are increased, while production of nucleotides, peptidoglycans, and phenolic glycolipids are reduced. The modified solution space of the alveolar macrophage and M. tb better represents the infectious state.

Second, the host-pathogen model more accurately predicts M. tb gene deletion tests than the current in vitro model, iNJ661. The host-pathogen model predicted 11 essential genes and 37 unessential genes differently than iNJ661. A total of 22 of the differentially predicted genes have been experimentally characterized (Sassetti and Rubin, 2003; Sohaskey, 2008). The host-pathogen model correctly predicted 18 of the 22 genes. Thus, iAB-AMØ-1410-Mt-661 is a more accurate platform for studying infectious states of M. tb.

Finally, we sought to determine metabolic differences in both the macrophage and M. tb between three different types of infection: latent, pulmonary, and meningeal. Transcription profiling data of the macrophage for the three infections (Thuong et al, 2008) were integrated in the context of the host–pathogen network to elucidate the reaction activity of the three infections. There was wide heterogeneity in the three infection states; some of these differences are highlighted. Macrophage hyaluronan synthase and export were only active in the pulmonary infection. This is potentially interesting from a pharmaceutical viewpoint as hyaluronan has been implicated as a potential carbon source for extracellular M. tb (Hirayama et al, 2009). In addition, we detected metabolic activity differences in M. tb pathways that have been previously discussed as potential drug targets (Eoh et al, 2007; Boshoff et al, 2008). Polyprenyl metabolic reactions were only active in the latent state infection, while de novo synthesis of nicotinamide cofactors was only active in latent and meningeal M. tb infections.

Host-pathogen modeling represents a novel approach for studying metabolic interactions during infection. iAB-AMØ-1410-Mt-661 is a more accurate platform for understanding the biology and pathophysiology of M. tb infection. Most importantly, genome-scale metabolic reconstructions can act as scaffolds for integrating high-throughput data. Particularly, in this study we were able to discern reaction activity differences between different infection types.

Metabolic coupling of Mycobacterium tuberculosis to its host is foundational to its pathogenesis. Computational genome-scale metabolic models have shown utility in integrating -omic as well as physiologic data for systemic, mechanistic analysis of metabolism. To date, integrative analysis of host–pathogen interactions using in silico mass-balanced, genome-scale models has not been performed. We, therefore, constructed a cell-specific alveolar macrophage model, iAB-AMØ-1410, from the global human metabolic reconstruction, Recon 1. The model successfully predicted experimentally verified ATP and nitric oxide production rates in macrophages. This model was then integrated with an M. tuberculosis H37Rv model, iNJ661, to build an integrated host–pathogen genome-scale reconstruction, iAB-AMØ-1410-Mt-661. The integrated host–pathogen network enables simulation of the metabolic changes during infection. The resulting reaction activity and gene essentiality targets of the integrated model represent an altered infectious state. High-throughput data from infected macrophages were mapped onto the host–pathogen network and were able to describe three distinct pathological states. Integrated host–pathogen reconstructions thus form a foundation upon which understanding the biology and pathophysiology of infections can be developed.

Magnesium depletion triggers production of an immune modulating diterpenoid in Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) is the causative agent of the human disease Tuberculosis, and remains a worldwide health threat responsible for ∼1.7 million deaths annually. During infection, Mtb prevents acidification of the engulfing phagosome, thus blocking endocytic progression and eventually leading to stable residence. The diterpenoid metabolite isotuberculosinol (isoTb) exhibits biological activity indicative of a role in this early arrest of phagosome maturation. Presumably, isoTb production should be induced by phagosomal entry. However, the relevant enzymatic genes are not transcriptionally upregulated during engulfment. Previous examination of the initial biosynthetic enzyme (Rv3377c/MtHPS) involved in isoTb biosynthesis revealed striking inhibition by its Mg(2+) cofactor, leading to the hypothesis that the depletion of Mg(2+) observed upon phagosomal engulfment may act to trigger isoTb biosynthesis. While Mtb is typically grown in relatively high levels of Mg(2+) (0.43 mM), shifting Mtb to media with phagosomal levels (0.1 mM) led to a significant (∼10-fold) increase in accumulation of the MtHPS product, halimadienyl diphosphate, as well as easily detectable amounts of the derived bioactive isoTb. These results demonstrate isoTb production by Mtb specifically under conditions that mimic phagosomal cation concentrations, and further support a role for isoTb in the Mtb infection process.

Copper resistance is essential for virulence of Mycobacterium tuberculosis

Copper (Cu) is essential for many biological processes, but is toxic when present in excessive amounts. In this study, we provide evidence that Cu plays a crucial role in controlling tuberculosis. A Mycobacterium tuberculosis (Mtb) mutant lacking the outer membrane channel protein Rv1698 accumulated 100-fold more Cu and was more susceptible to Cu toxicity than WT Mtb. Similar phenotypes were observed for a M. smegmatis mutant lacking the homolog Ms3747, demonstrating that these mycobacterial copper transport proteins B (MctB) are essential for Cu resistance and maintenance of low intracellular Cu levels. Guinea pigs responded to infection with Mtb by increasing the Cu concentration in lung lesions. Loss of MctB resulted in a 1,000- and 100-fold reduced bacterial burden in lungs and lymph nodes, respectively, in guinea pigs infected with Mtb. In mice, the persistence defect of the Mtb mctB mutant was exacerbated by the addition of Cu to the diet. These experiments provide evidence that Cu is used by the mammalian host to control Mtb infection and that Cu resistance mechanisms are crucial for Mtb virulence. Importantly, Mtb is much more susceptible to Cu than other bacteria and is killed in vitro by Cu concentrations lower than those found in phagosomes of macrophages. Hence, this study reveals an Achilles heel of Mtb that might be a promising target for tuberculosis chemotherapy.

The Mycobacterium tuberculosis membrane protein Rv0180c: Evaluation of peptide sequences implicated in mycobacterial invasion of two human cell lines

The identification and characterization of hypothetical membrane proteins from Mycobacterium tuberculosis have led to a better understanding of the mechanisms used by this pathogen to invade and survive inside host cells. This study assessed the presence, transcription, localization and possible biological activity of the conserved hypothetical protein Rv0180c from M. tuberculosis. Bioinformatics analyses indicated that Rv0180c contains a signal peptide, six possible transmembrane helices and a Plasmodium Export Element (PEXEL)-like motif. PCR analyses showed the presence of the Rv0180c gene in strains from the M. tuberculosis complex; but transcription was not detected in Mycobacterium microti. Sera against synthetic peptides of Rv0180c recognized two protein bands in M. tuberculosis H37Rv sonicate: a ∼48-kDa band close to the predicted molecular mass of Rv0180c (47.6 kDa), and a 63-kDa band probably caused by protein modifications. Moreover, the same sera located the protein on the surface of M. tuberculosis H37Rv bacilli by immunoelectron microscopy. Twenty-three synthetic peptides spanning the entire length of Rv0180c were tested for their ability to bind to U937 and A549 cells, finding nine high-activity binding peptides (HABPs) specific for both cell types, two HABPs specific for A549 cells (namely 31032 and 31044) and two HABPs specific for U937 cells (namely 31025 and 31041). HABPs inhibited invasion of M. tuberculosis H37Rv into A549 or U937 cells by significant percentages and facilitated internalization of latex beads in A549 cells. The Rv0180c HABPs herein reported could be preliminary candidates to be assessed as components of a multiepitope, chemically synthesized, subunit-based vaccine against tuberculosis.

Transcriptional profiling of mycobacterium tuberculosis during infection: lessons learned

Infection with Mycobacterium tuberculosis, the causative agent of tuberculosis, is considered one of the biggest infectious disease killers worldwide. A significant amount of attention has been directed toward revealing genes involved in the virulence and pathogenesis of this air-born pathogen. With the advances in technologies for transcriptional profiling, several groups, including ours, took advantage of DNA microarrays to identify transcriptional units differentially regulated by M. tuberculosis within a host. The main idea behind this approach is that pathogens tend to regulate their gene expression levels depending on the host microenvironment, and preferentially express those needed for survival. Identifying this class of genes will improve our understanding of pathogenesis. In our case, we identified an in vivo expressed genomic island that was preferentially active in murine lungs during early infection, as well as groups of genes active during chronic tuberculosis. Other studies have identified additional gene groups that are active during macrophage infection and even in human lungs. Despite all of these findings, one of the lingering questions remaining was whether in vivo expressed transcripts are relevant to the virulence, pathogenesis, and persistence of the organism. The work of our group and others addressed this question by examining the contribution of in vivo expressed genes using a strategy based on gene deletions followed by animal infections. Overall, the analysis of most of the in vivo expressed genes supported a role of these genes in M. tuberculosis pathogenesis. Further, these data suggest that in vivo transcriptional profiling is a valid approach to identify genes required for bacterial pathogenesis.

A novel copper-responsive regulon in Mycobacterium tuberculosis

In this work we describe the identification of a copper-inducible regulon in Mycobacterium tuberculosis (Mtb). Among the regulated genes was Rv0190/MT0200, a paralogue of the copper metalloregulatory repressor CsoR. The five-locus regulon, which includes a gene that encodes the copper-protective metallothionein MymT, was highly induced in wild-type Mtb treated with copper, and highly expressed in an Rv0190/MT0200 mutant. Importantly, the Rv0190/MT0200 mutant was hyper-resistant to copper. The promoters of all five loci share a palindromic motif that was recognized by the gene product of Rv0190/MT0200. For this reason we named Rv0190/MT0200 RicR for regulated in copper repressor. Intriguingly, several of the RicR-regulated genes, including MymT, are unique to pathogenic Mycobacteria. The identification of a copper-responsive regulon specific to virulent mycobacterial species suggests copper homeostasis must be maintained during an infection. Alternatively, copper may provide a cue for the expression of genes unrelated to metal homeostasis, but nonetheless necessary for survival in a host.

Models for antitubercular activity of 5â-O-[(N-Acyl)sulfamoyl]adenosines

The relationship between topological indices and antitubercular activity of 5â-O-[(N-Acyl)sulfamoyl]adenosines has been investigated. A data set consisting of 31 analogues of 5â-O-[(N-Acyl)sulfamoyl]adenosines was selected for the present study. The values of numerous topostructural and topochemical indices for each of 31 differently substituted analogues of the data set were computed using an in-house computer program. Resulting data was analyzed and suitable models were developed through decision tree, random forest and moving average analysis (MAA). The goodness of the models was assessed by calculating overall accuracy of prediction, sensitivity, specificity and Mathews correlation coefficient. Pendentic eccentricity index â a novel highly discriminating, non-correlating pendenticity based topochemical descriptor â was also conceptualized and successfully utilized for the development of a model for antitubercular activity of 5â-O-[(N-Acyl)sulfamoyl]adenosines. The proposed index exhibited not only high sensitivity towards both the presence as well as relative position(s) of pendent/heteroatom(s) but also led to significant reduction in degeneracy. Random forest correctly classified the analogues into active and inactive with an accuracy of 67.74%. A decision tree was also employed for determining the importance of molecular descriptors. The decision tree learned the information from the input data with an accuracy of 100% and correctly predicted the cross-validated (10 fold) data with accuracy up to 77.4%. Statistical significance of proposed models was also investigated using intercorrelation analysis. Accuracy of prediction of proposed MAA models ranged from 90.4 to 91.6%.

Elucidation of the functional metal binding profile of a Cd(II)/Pb(II) sensor CmtR(Sc) from Streptomyces coelicolor

Metal homeostasis and resistance in bacteria is maintained by a panel of metal-sensing transcriptional regulators that collectively control transition metal availability and mediate resistance to heavy metal xenobiotics, including As(III), Cd(II), Pb(II), and Hg(II). The ArsR family constitutes a superfamily of metal sensors that appear to conform to the same winged helical, homodimeric fold, that collectively "sense" a wide array of beneficial metal ions and heavy metal pollutants. The genomes of many actinomycetes, including the soil dwelling bacterium Streptomyces coelicolor and the human pathogen Mycobacterium tuberculosis, encode over ten ArsR family regulators, most of unknown function. Here, we present the characterization of a homologue of M. tuberculosis CmtR (CmtR(Mtb)) from S. coelicolor, denoted CmtR(Sc). We show that CmtR(Sc), in contrast to CmtR(Mtb), binds two monomer mol equivalents of Pb(II) or Cd(II) to form two pairs of sulfur-rich coordination complexes per dimer. Metal site 1 conforms exactly to the alpha4C site previously characterized in CmtR(Mtb) while metal site 2 is coordinated by a C-terminal vicinal thiolate pair, Cys110 and Cys111. Biological assays reveal that only Cd(II) and, to a lesser extent, Pb(II) mediate transcriptional derepression in the heterologous host Mycobacterium smegmatis in a way that requires metal site 1. In contrast, mutagenesis of metal site 2 ligands Cys110 or Cys111 significantly reduces Cd(II) responsiveness, with no detectable effect on Pb(II) sensing. The implications of these findings on the ability to predict metal specificity and function from metal-site signatures in the primary structure of ArsR family proteins are discussed.

Virulence-related Mycobacterium avium subsp hominissuis MAV_2928 gene is associated with vacuole remodeling in macrophages

Background

Mycobacterium avium subsp hominissuis (previously Mycobacterium avium subsp avium) is an environmental organism associated with opportunistic infections in humans. Mycobacterium hominissuis infects and replicates within mononuclear phagocytes. Previous study characterized an attenuated mutant in which the PPE gene (MAV_2928) homologous to Rv1787 was inactivated. This mutant, in contrast to the wild-type bacterium, was shown both to have impaired the ability to replicate within macrophages and to have prevented phagosome/lysosome fusion.

Results

MAV_2928 gene is primarily upregulated upon phagocytosis. The transcriptional profile of macrophages infected with the wild-type bacterium and the mutant were examined using DNA microarray, which showed that the two bacteria interact uniquely with mononuclear phagocytes. Based on the results, it was hypothesized that the phagosome environment and vacuole membrane of the wild-type bacterium might differ from the mutant. Wild-type bacterium phagosomes expressed a number of proteins different from those infected with the mutant. Proteins on the phagosomes were confirmed by fluorescence microscopy and Western blot. The environment in the phagosome of macrophages infected with the mutant differed from the environment of vacuoles with M. hominissuis wild-type in the concentration of zinc, manganese, calcium and potassium.

Conclusion

The results suggest that the MAV_2928 gene/operon might participate in the establishment of bacterial intracellular environment in macrophages.

Identification of virulence determinants of Mycobacterium avium that impact on the ability to resist host killing mechanisms

Mycobacterium avium is an opportunistic pathogen associated with pulmonary disease in non-AIDS patients and disseminated infection in patients with AIDS. The chief route of infection is by colonization and invasion of the mucosa of the gastrointestinal tract, but infection through the respiratory route also occurs. After crossing the mucosa, M. avium infects and replicates within tissue macrophages. To identify M. avium genes required for survival in vivo, a library of signature-tagged transposon mutants was constructed and screened for clones attenuated in mice. Thirty-two clones were found to be attenuated for their virulence, from which eleven were sequenced and tested further. All the mutants studied grew similarly in vitro to the wild-type MAC104. Ten mutants were tested individually in mice, confirming the attenuated phenotype. MAV_2450, a polyketide synthase homologue to Mycobacterium tuberculosis pks12, was identified. STM5 and STM10 genes (encoding two hypothetical proteins MAV_4292 and MAV_4012) were associated with susceptibility to oxidative products. Mutants MAV_2450, MAV_4292, MAV_0385 and MAV_4264 live in macrophage vacuoles with acidic pH (below 6.9). Mutants MAV_4292, MAV_0385 and MAV_4264 were susceptible to nitric oxide in vitro. The study of individual mutants can potentially lead to new knowledge about M. avium pathogenic mechanisms.

A role for the ATP7A copper-transporting ATPase in macrophage bactericidal activity

Copper is an essential micronutrient that is necessary for healthy immune function. This requirement is underscored by an increased susceptibility to bacterial infection in copper-deficient animals; however, a molecular understanding of its importance in immune defense is unknown. In this study, we investigated the effect of proinflammatory agents on copper homeostasis in RAW264.7 macrophages. Interferon-gamma was found to increase expression of the high affinity copper importer, CTR1, and stimulate copper uptake. This was accompanied by copper-stimulated trafficking of the ATP7A copper exporter from the Golgi to vesicles that partially overlapped with phagosomal compartments. Silencing of ATP7A expression attenuated bacterial killing, suggesting a role for ATP7A-dependent copper transport in the bactericidal activity of macrophages. Significantly, a copper-sensitive mutant of Escherichia coli lacking the CopA copper-transporting ATPase was hypersensitive to killing by RAW264.7 macrophages, and this phenotype was dependent on ATP7A expression. Collectively, these data suggest that copper-transporting ATPases, CopA and ATP7A, in both bacteria and macrophage are unique determinants of bacteria survival and identify an unexpected role for copper at the host-pathogen interface.

Protein turnover in mycobacterial proteomics

Understanding the biology of Mycobacterium tuberculosis is one of the primary challenges in current tuberculosis research. Investigation of mycobacterial biology using the systems biology approach has deciphered much information with regard to the bacilli and tuberculosis pathogenesis. The modulation of its environment and the ability to enter a dormant phase are the hallmarks of M. tuberculosis. Until now, proteome studies have been able to understand much about the role of various proteins, mostly in growing M. tuberculosis cells. It has been difficult to study dormant M. tuberculosis by conventional proteomic techniques with very few proteins being found to be differentially expressed. Discrepancy between proteome and transcriptome studies lead to the conclusion that a certain aspect of the mycobacterial proteome is not being explored. Analysis of protein turnover may be the answer to this dilemma. This review, while giving a gist of the proteome response of mycobacteria to various stresses, analyzes the data obtained from abundance studies versus data from protein turnover studies in M. tuberculosis. This review brings forth the point that protein turnover analysis is capable of discerning more subtle changes in protein synthesis, degradation, and secretion activities. Thus, turnover studies could be incorporated to provide a more in-depth view into the proteome, especially in dormant or persistent cells. Turnover analysis might prove helpful in drug discovery and a better understanding of the dynamic nature of the proteome of mycobacteria.

Identification and functional characterization of the iron-dependent regulator (IdeR) of Mycobacterium avium subsp. paratuberculosis

Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne's disease in cattle and sheep, has unique iron requirements in that it is mycobactin-dependent for cultivation in vitro. The iron-dependent regulator (IdeR) is a well-characterized global regulator responsible for maintaining iron homeostasis in Mycobacterium tuberculosis (MTB). We identified an orthologous segment in the MAP genome, MAP2827, with >93 % amino acid identity to MTB IdeR. Electrophoretic mobility shift assays and DNase protection assays confirmed that MAP2827 binds the 19 bp consensus motif (iron box) on the MAP genome. Sequencing of MAP2827 from multiple isolates revealed a non-synonymous change (R91G) exclusive to sheep strains. Reporter gene assays and quantitative real-time RT-PCR assays in two diverse MAP strains and in an ideR deletion mutant of M. smegmatis (mc(2)155) suggested that both sheep MAP IdeR (sIdeR) and cattle MAP IdeR (cIdeR) repress mbtB transcription at high iron concentrations and relieve repression at low iron concentrations. On the other hand, bfrA (an iron storage gene) was upregulated by cIdeR when presented with MTB or the cattle MAP bfrA promoter, and was downregulated by sIdeR in the presence of MTB, or sheep or cattle MAP bfrA promoters, at high iron concentrations. The differential iron regulatory mechanisms between IdeR-regulated genes across strains may contribute to the differential growth or pathogenic characteristics of sheep and cattle MAP strains. Taken together, our study provides a possible reason for mycobactin dependency and suggests strong implications in the differential iron acquisition and storage mechanisms in MAP.

Characterization and inhibition of a class II diterpene cyclase from Mycobacterium tuberculosis: implications for tuberculosis

Mycobacterium tuberculosis remains a widespread and devastating human pathogen, whose ability to infiltrate macrophage host cells from the human immune system is an active area of investigation. We have recently reported the discovery of a novel diterpene from M. tuberculosis, edaxadiene, whose ability to arrest phagosomal maturation in isolation presumably contributes to this critical process in M. tuberculosis infections. (Mann, F. M., Xu, M., Chen, X., Fulton, D. B., Russell, D. G., and Peters, R. J. (2009) J. Am. Chem. Soc., in press). Here, we present characterization of the class II diterpene cyclase that catalyzes the committed step in edaxadiene biosynthesis, i.e. the previously identified halimadienyl-diphosphate synthase (HPS; EC 5.5.1.16). Intriguingly, our kinetic analysis suggests a potential biochemical regulatory mechanism that triggers edaxadiene production upon phagosomal engulfment. Furthermore, we report characterization of potential HPS inhibitors: specifically, two related transition state analogs (15-aza-14,15-dihydrogeranylgeranyl diphosphate (7a) and 15-aza-14,15-dihydrogeranylgeranyl thiolodiphosphate (7b)) that exhibit very tight binding. Although arguably not suitable for clinical use, these nevertheless provide a basis for pharmaceutical design against this intriguing biosynthetic pathway. Finally, we provide evidence indicating that this pathway exists only in M. tuberculosis and is not functional in the closely related Mycobacterium bovis because of an inactivating frameshift in the HPS-encoding gene. Thus, we hypothesize that the inability to produce edaxadiene may be a contributing factor in the decreased infectivity and/or virulence of M. bovis relative to M. tuberculosis in humans.

Impairment of d-alanine biosynthesis in Mycobacterium smegmatis determines decreased intracellular survival in human macrophages

d-Alanine is a structural component of mycobacterial peptidoglycan. The primary route of d-alanine biosynthesis in eubacteria is the enantiomeric conversion from l-alanine, a reaction catalysed by d-alanine racemase (Alr). Mycobacterium smegmatis alr insertion mutants are not dependent on d-alanine for growth and display a metabolic pattern consistent with an alternative pathway for d-alanine biosynthesis. In this study, we demonstrate that the M. smegmatis alr insertion mutant TAM23 can synthesize d-alanine at lower levels than the parental strain. The insertional inactivation of the alr gene also decreases the intracellular survival of mutant strains within primary human monocyte-derived macrophages. By complementation studies, we confirmed that the impairment of alr gene function is responsible for this reduced survival. Inhibition of superoxide anion and nitric oxide formation in macrophages suppresses the differential survival. In contrast, for bacteria grown in broth, both strains had approximately the same susceptibility to hydrogen peroxide, acidified sodium nitrite, low pH and polymyxin B. In contrast, TAM23 exhibited increased resistance to lysozyme. d-Alanine supplementation considerably increased TAM23 viability in nutritionally deficient media and within macrophages. These results suggest that nutrient deprivation in phagocytic cells combined with killing mediated by reactive intermediates underlies the decreased survival of alr mutants. This knowledge may be valuable in the construction of mycobacterial auxotrophic vaccine candidates.

TB vaccines: current status and future perspectives

Vaccines against intracellular pathogens such as Mycobacterium tuberculosis need to induce strong cellular immune responses. Antigen discovery programs have exploited this and used proteome studies and T-cell recognition in PPD-positive individuals to select proteins and after testing for protective efficacy in animals the most promising proteins have been put together in fusion molecules. Three such fusion proteins are currently in clinical trials, the two most advanced have already passed phase I trials and are entering phase II.

The potassium transporter Trk and external potassium modulate Salmonella enterica protein secretion and virulence

Potassium (K(+)) is the most abundant intracellular cation and is essential for many physiological functions of all living organisms; however, its role in the pathogenesis of human pathogens is not well understood. In this study, we characterized the functions of the bacterial Trk K(+) transport system and external K(+) in the pathogenesis of Salmonella enterica, a major food-borne bacterial pathogen. Here we report that Trk is important for Salmonella to invade and grow inside epithelial cells. It is also necessary for the full virulence of Salmonella in an animal infection model. Analysis of proteins of Salmonella indicated that Trk is involved in the expression and secretion of effector proteins of the type III secretion system (TTSS) encoded by Salmonella pathogenicity island 1 (SPI1) that were previously shown to be necessary for Salmonella invasion. In addition to the role of the Trk transporter in the pathogenesis of Salmonella, we discovered that external K(+) modulates the pathogenic properties of Salmonella by increasing the expression and secretion of effector proteins of the SPI1-encoded TTSS and by enhancing epithelial cell invasion. Our studies demonstrated that K(+) is actively involved in the pathogenesis of Salmonella and indicated that Salmonella may take advantage of the high K(+) content inside host cells and in the intestinal fluid during diarrhea to become more virulent.