Tissue inhibitor of metalloproteinases‐1‐induced scattered liver metastasis is mediated by host‐derived urokinase‐type plasminogen activator

Paradoxically, not only proteinases but also their inhibitors can correlate with bad prognosis of cancer patients, underlining the evolving concept of the protease web as the complex interplay between proteinases, their inhibitors and effector molecules. Elevated levels of tissue inhibitor of metalloproteinases‐1 (TIMP‐1) render the liver more susceptible to metastasis by triggering urokinase plasminogen activator (uPA) expression as well as hepatocyte growth factor (HGF) signalling, thereby leading to the fatal scattered infiltration of metastasizing tumour cells throughout the parenchyma of the target organ. Here, we investigated whether host uPA is a crucial protagonist for the TIMP‐1‐induced modulation of a pro‐metastatic microenvironment in the liver. Indeed, in livers of uPA‐ablated mice elevated TIMP‐1 levels did not trigger HGF signalling and did not promote metastasis of a murine T‐lymphoma cell line. In contrast, lack of tumour cell‐derived uPA induced by gene silencing did not interfere with this pro‐metastatic pathway. Furthermore, host uPA was necessary for the recruitment of neutrophilic granulocytes and the associated increase of HGF in livers with elevated TIMP‐1 levels. This newly identified co‐operation between TIMP‐1 and host uPA suggests that therapies, simultaneously interfering with pro‐ and anti‐proteolytic pathways may be beneficial for patients with metastatic disease.     

The Mycobacterium bovis Bacille Calmette-Gu��rin Phagosome Proteome

Mycobacterium tuberculosis and Mycobacterium bovis bacille Calmette-Guérin (BCG) alter the maturation of their phagosomes and reside within a compartment that resists acidification and fusion with lysosomes. To define the molecular composition of this compartment, we developed a novel method for obtaining highly purified phagosomes from BCG-infected human macrophages and analyzed the phagosomes by Western immunoblotting and mass spectrometry-based proteomics. Our purification procedure revealed that BCG grown on artificial medium becomes less dense after growth in macrophages. By Western immunoblotting, LAMP-2, Niemann-Pick protein C1, and syntaxin 3 were readily detectable on the BCG phagosome but at levels that were lower than on the latex bead phagosome; flotillin-1 and the vacuolar ATPase were barely detectable on the BCG phagosome but highly enriched on the latex bead phagosome. Immunofluorescence studies confirmed the scarcity of flotillin on BCG phagosomes and demonstrated an inverse correlation between bacterial metabolic activity and flotillin on M. tuberculosis phagosomes. By mass spectrometry, 447 human host proteins were identified on BCG phagosomes, and a partially overlapping set of 289 human proteins on latex bead phagosomes was identified. Interestingly, the majority of the proteins identified consistently on BCG phagosome preparations were also identified on latex bead phagosomes, indicating a high degree of overlap in protein composition of these two compartments. It is likely that many differences in protein composition are quantitative rather than qualitative in nature. Despite the remarkable overlap in protein composition, we consistently identified a number of proteins on the BCG phagosomes that were not identified in any of our latex bead phagosome preparations, including proteins involved in membrane trafficking and signal transduction, such as Ras GTPase-activating-like protein IQGAP1, and proteins of unknown function, such as FAM3C. Our phagosome purification procedure and initial proteomics analyses set the stage for a quantitative comparative analysis of mycobacterial and latex bead phagosome proteomes.Mycobacterium tuberculosis, the etiological agent of tuberculosis, is a facultative intracellular bacterium. In human macrophages, M. tuberculosis resides in a membrane-bound phagosomal compartment that resists fusion with lysosomes and is only mildly acidified (1–5). In previous studies, using the cryosection immunogold technique, we have found that the M. tuberculosis phagosome exhibits delayed clearance of major histocompatability complex class I molecules and relatively weak staining for lysosomal membrane glycoproteins CD63, LAMP-1,¹ and LAMP-2 and the lysosomal acid protease cathepsin D (6–10). Studies by other investigators have also demonstrated that M. tuberculosis and other mycobacterial species, including Mycobacterium bovis BCG, reside in phagosomes that resist acidification, are less mature, and less fusogenic with lysosomes than phagosomes containing inert particles (11–13). These results are consistent with the hypothesis that M. tuberculosis and M. bovis BCG retard the maturation of their phagosomes along the endolysosomal pathway and reside in a compartment that has not matured fully to a phagolysosome (7). Although the phagosomes of latex beads have been subjected to detailed proteomics analysis by Desjardins and co-workers (14), a detailed proteomics study of the M. bovis BCG phagosome has not been reported previously.We describe in this study a novel method for the purification of the BCG phagosome from infected human macrophages, a detailed proteomics analysis of the BCG phagosome, and a comparison of the phagosome with latex bead phagosomes isolated from human macrophages. This study is the first comprehensive proteomics study of the M. bovis BCG phagosome and the first mass spectrometry-based proteomics study of the latex bead phagosome in human macrophages. We showed by Western immunoblotting that, relative to latex bead phagosomes, the BCG phagosome is relatively depleted in LAMP-2, NPC1, flotillin-1, vATPase, and syntaxin 3. Remarkably, by mass spectrometry, we documented a high degree of overlap in the set of proteins on BCG and latex bead phagosomes but also noteworthy differences. Novel proteins detected on the BCG phagosome but not on the latex bead phagosome include CD44, intercellular adhesion molecule 1, protein FAM3C, Ral-A/Ral-B, stress-induced phosphoprotein 1, band 4.1-like protein 3, septin-7, Ras GTPase-activating protein-like protein IQGAP1, Rab-6A, erlin-2, and tumor protein D54. Conversely, proteins identified on latex bead phagosomes but not on the BCG phagosome are β-galactosidase and sialate O-acetylesterase.     

Targeted Quantitation of Site-Specific Cysteine Oxidation in Endogenous Proteins Using a Differential Alkylation and Multiple Reaction Monitoring Mass Spectrometry Approach

Reactive oxygen species (ROS) are both physiological intermediates in cellular signaling and mediators of oxidative stress. The cysteine-specific redox-sensitivity of proteins can shed light on how ROS are regulated and function, but low sensitivity has limited quantification of the redox state of many fundamental cellular regulators in a cellular context. Here we describe a highly sensitive and reproducible oxidation analysis approach (OxMRM) that combines protein purification, differential alkylation with stable isotopes, and multiple reaction monitoring mass spectrometry that can be applied in a targeted manner to virtually any cysteine or protein. Using this approach, we quantified the site-specific cysteine oxidation status of endogenous p53 for the first time and found that Cys182 at the dimerization interface of the DNA binding domain is particularly susceptible to diamide oxidation intracellularly. OxMRM enables analysis of sulfinic and sulfonic acid oxidation levels, which we validate by assessing the oxidation of the catalytic Cys215 of protein tyrosine phosphatase-1B under numerous oxidant conditions. OxMRM also complements unbiased redox proteomics discovery studies as a verification tool through its high sensitivity, accuracy, precision, and throughput.Oxidation of cysteine residues plays a critical role in modifying the structure and function of many proteins. Although cysteine oxidation is a tightly regulated biological process, nonenzymatic processes can contribute substantially to its levels, such as during oxidative stress. Regulatory oxidation states such as disulfide bonding and S-nitrosylation are readily modulated (1) and play an essential role in many physiological processes, including cell cycle, growth, death, and differentiation (2). In contrast, prolonged accumulation of reactive oxygen species is associated with many pathological conditions and leads to stable overoxidized states (sulfinic and sulfonic acid) that may disrupt redox regulation and protein function (3) and, in most cases, are thought to be nonregenerative.Assays capable of comprehensively assessing the dynamic changes in site-specific oxidation states are especially critical to understanding the contribution of redox status to many diseases. Numerous redox-sensitive proteins, including essential cellular regulators such as p53, have been described previously (for review, see ref. 4). However, technical factors have hampered the identification of specific site(s) of modification and characterization of their redox status in cells. Site-directed mutagenesis is often employed to determine whether specific cysteines have redox-regulated functional roles (1), but this approach provides no information on the oxidation status of the endogenous protein. In addition, cysteine oxidation is dynamically dependent on the concentration, location, and specificity of small-molecule oxidants (5) and regulators of various antioxidant enzymes (6). Thiol pKa (7), solvent accessibility, and subcellular compartment (8, 9) also contribute to the dynamics of cysteine oxidation. Because the interface between chronic oxidative stress and disruption of essential cellular signaling has substantial biological relevance to disease and age-related pathological conditions (10–13), there is a strong need to develop sensitive and flexible assays capable of quantifying dynamic changes in the redox status of specific endogenous proteins.Direct analysis of most regulatory cysteine modifications is not suitable for robust quantitation because the modifications tend to be labile and susceptible to artifactual changes. Accurate preservation of the thiol oxidation state is commonly achieved with a three-step differential alkylation labeling strategy in which nonoxidized cysteines are 1) labeled with a tag, 2) chemically reduced, and 3) labeled with a distinguishing tag. The value of this process is that it replaces the labile oxidation-modified cysteines with highly stable alkylated forms (1). Differential alkylation specifically targets cysteine oxidation species that are susceptible to reaction with chemical reductants (DTT or TCEP¹) because higher oxidation states such as sulfinic and sulfonic acid are chemically irreversible. Fluorescent or epitope tags have been employed to evaluate redox sensitivity at the protein level (14, 15); however, combining differential alkylation using stable isotope-labeled reagents with mass spectrometry simultaneously identifies the specifically oxidized site and quantifies its reversible oxidation status. Although labeled iodoacetic acid (16) and N-ethylmaleimide (17) (NEM) have often been used, commercial ICAT reagents have become the preferred stable isotope label for redox analysis (18–21). A recent ICAT-based study identified and quantified the reversible oxidation of 120 redox-sensitive cysteines in Escherichia coli in an unbiased manner (18). However, because of the limited sensitivity, dynamic range, number of testable conditions, and stochastic sampling inherent in unbiased proteomics experiments, this approach has limited utility for interrogating targeted moderate- to low-abundance proteins or comprehensively characterizing multiple cysteines within a single protein. The use of an ICAT-based approach for targeted analysis of specific proteins is significantly limited by both the difficulty in scaling down the ICAT protocol and the disruption of protein structure that occurs after alkylation with numerous ICAT adducts, each over a kilodalton in size, which may occlude antibody epitopes useful for immunoaffinity enrichment.To overcome these limitations, we developed a highly sensitive method, OxMRM, that integrates protein purification, differential alkylation using a generic d₅ stable isotope-labeled NEM, and multiple reaction monitoring (MRM). OxMRM can quantify the oxidation status, both reversible and irreversible, of virtually any targeted cysteine or protein, even if in low abundance. We validate the OxMRM approach using the low-abundance tumor suppressor protein p53 and an established overoxidizable signaling regulator, protein tyrosine phosphatase-1B (PTP1B) (22, 23). These proteins serve as benchmark examples of nuclear and cytoplasmic redox-regulated proteins bearing reversibly and irreversibly oxidized cysteines. The flexibility of the OxMRM method allows it to be applied to essentially any protein or cysteine of interest with equal ease, allowing in-depth, site-specific analysis of putative and established redox-sensitive proteins. This makes OxMRM an ideal complement to large-scale redox proteomics studies as a verification tool with high sensitivity, precision, accuracy, and capacity to assess numerous oxidation conditions.     

Optimal Strategy for Competence Differentiation in Bacteria

A phylogenetically diverse subset of bacterial species are naturally competent for transformation by DNA. Transformation entails recombination of genes between different lineages, representing a form of bacterial sex that increases standing genetic variation. We first assess whether homologous recombination by transformation is favored by evolution. Using stochastic population genetic computer simulations in which beneficial and deleterious mutations occur at many loci throughout the whole genome, we find that transformation can increase both the rate of adaptive evolution and the equilibrium level of fitness. Secondly, motivated by experimental observations of Bacillus subtilis, we assume that competence additionally entails a weak persister phenotype, i.e., the rates of birth and death are reduced for these cells. Consequently, persisters evolve more slowly than non-persisters. We show via simulation that strains which stochastically switch into and out of the competent phenotype are evolutionarily favored over strains that express only a single phenotype. Our model''s simplicity enables us to derive and numerically solve a system of finite- deterministic equations that describe the evolutionary dynamics. The observed tradeoff between the benefit of recombination and the cost of persistence may explain the previously mysterious observation that only a fractional subpopulation of B. subtilis cells express competence. More generally, this work demonstrates that population genetic forces can give rise to phenotypic diversity even in an unchanging and homogeneous environment.     

Cell-free expression as an emerging technique for the large scale production of integral membrane protein

Membrane proteins are highly underrepresented in structural data banks due to tremendous difficulties that occur upon approaching their structural analysis. Inefficient sample preparation from conventional cellular expression systems is in many cases the first major bottleneck. Preparative scale cell-free expression has now become an emerging alternative tool for the high level production of integral membrane proteins. Many toxic effects attributed to the overproduction of recombinant proteins are eliminated by cell-free expression as viable host cells are no longer required. A unique characteristic is the open nature of cell-free systems that offers a variety of options to manipulate the reaction conditions in order to protect or to stabilize the synthesized recombinant proteins. Detergents or lipids can easily be supplemented and membrane proteins can therefore be synthesized directly into a defined hydrophobic environment of choice that permits solubility and allows the functional folding of the proteins. Alternatively, cell-free produced precipitates of membrane proteins can efficiently be solubilized in mild detergents after expression. Highly valuable for structural approaches is the fast and efficient cell-free production of uniformly or specifically labeled proteins. A considerable number of membrane proteins from diverse families like prokaryotic small multidrug transporters or eukaryotic G-protein coupled receptors have been produced in cell-free systems in high amounts and in functionally active forms. We will give an overview about the current state of the art of this new approach with special emphasis on technical aspects as well as on the functional and structural characterization of cell-free produced membrane proteins.     

A simple and rapid protein array based method for the simultaneous detection of biowarfare agents

A protein chip has been developed that allows the simultaneous detection of a multitude of different biowarfare agents. The chip was developed for the ArrayTube platform providing a cheap and easy to handle technology solution that combines a microtube-integrated protein chip with the classical procedure of a sandwich-enzyme-linked immunosorbent assay and signal amplification by streptavidin-poly-horseradish peroxidase. Specific immunoassays for Staphylococcus enterotoxin B, ricin, Venezuelan equine encephalitis virus, St. Louis encephalitis virus, West Nile virus, Yellow fever virus, Orthopox virus species, Francisella tularensis, Yersinia pestis, Brucella melitensis, Burkholderia mallei and Escherichia coli EHEC O157:H7 were developed and optimized. All assays could be completed within 1 to 1 1/2 h and detection levels were demonstrated to be as low as in well established ELISAs. Most interesting, as a result of careful antibody screening and testing, it is currently possible to analyse at least five of the "dirty dozen" agents on one single protein chip in parallel.