A Pseudomonas aeruginosa TIR effector mediates immune evasion by targeting UBAP1 and TLR adaptors

Bacterial pathogens often subvert the innate immune system to establish a successful infection. The direct inhibition of downstream components of innate immune pathways is particularly well documented but how bacteria interfere with receptor proximal events is far less well understood. Here, we describe a Toll/interleukin 1 receptor (TIR) domain‐containing protein (PumA) of the multi‐drug resistant Pseudomonas aeruginosa PA7 strain. We found that PumA is essential for virulence and inhibits NF‐κB, a property transferable to non‐PumA strain PA14, suggesting no additional factors are needed for PumA function. The TIR domain is able to interact with the Toll‐like receptor (TLR) adaptors TIRAP and MyD88, as well as the ubiquitin‐associated protein 1 (UBAP1), a component of the endosomal‐sorting complex required for transport I (ESCRT‐I). These interactions are not spatially exclusive as we show UBAP1 can associate with MyD88, enhancing its plasma membrane localization. Combined targeting of UBAP1 and TLR adaptors by PumA impedes both cytokine and TLR receptor signalling, highlighting a novel strategy for innate immune evasion.     

PILOT_PROTEIN: Identification of Unmodified and Modified Proteins via High-Resolution Mass Spectrometry and Mixed-Integer Linear Optimization

A novel protein identification framework, PILOT_PROTEIN, has been developed to construct a comprehensive list of all unmodified proteins that are present in a living sample. It uses the peptide identification results from the PILOT_SEQUEL algorithm to initially determine all unmodified proteins within the sample. Using a rigorous biclustering approach that groups incorrect peptide sequences with other homologous sequences, the number of false positives reported is minimized. A sequence tag procedure is then incorporated along with the untargeted PTM identification algorithm, PILOT_PTM, to determine a list of all modification types and sites for each protein. The unmodified protein identification algorithm, PILOT_PROTEIN, is compared to the methods SEQUEST, InsPecT, X!Tandem, VEMS, and ProteinProspector using both prepared protein samples and a more complex chromatin digest. The algorithm demonstrates superior protein identification accuracy with a lower false positive rate. All materials are freely available to the scientific community at http://pumpd.princeton.edu .     

A Mixed Integer Linear Optimization Framework for the Identification and Quantification of Targeted Post-translational Modifications of Highly Modified Proteins Using Multiplexed Electron Transfer Dissociation Tandem Mass Spectrometry

Here we present a novel methodology for the identification of the targeted post-translational modifications present in highly modified proteins using mixed integer linear optimization and electron transfer dissociation (ETD) tandem mass spectrometry. For a given ETD tandem mass spectrum, the rigorous set of modified forms that satisfy the mass of the precursor ion, within some tolerance error, are enumerated by solving a feasibility problem via mixed integer linear optimization. The enumeration of the entire superset of modified forms enables the method to normalize the relative contributions of the individual modification sites. Given the entire set of modified forms, a superposition problem is then formulated using mixed integer linear optimization to determine the relative fractions of the modified forms that are present in the multiplexed ETD tandem mass spectrum. Chromatographic information in the mass and time dimension is utilized to assess the likelihood of the assigned modification states, to average several tandem mass spectra for confident identification of lower level forms, and to infer modification states of partially assigned spectra. The utility of the proposed computational framework is demonstrated on an entire LC-MS/MS ETD experiment corresponding to a mixture of highly modified histone peptides. This new computational method will facilitate the unprecedented LC-MS/MS ETD analysis of many hypermodified proteins and offer novel biological insight into these previously understudied systems.Accurate identification of post-translational modifications (PTMs)¹ is a critical and often difficult task in proteomics. Most standard mass spectrometry-based techniques for the identification of protein modifications utilize a “bottom up” approach where the proteins are enzymatically digested into smaller peptides that are subsequently ionized and fragmented via CID to derive their sequence information (1–9). The identification of all the modifications present in a protein hinges on the successful identification of the PTM modifications of its corresponding peptides. This protocol can be limited by (a) insufficient elution and detection of all the peptides that cover the entire sequence of the protein, (b) false or incomplete identifications at the peptide level, and (c) the existence of different modification states of the same protein. Additional complications arise when using CID to study labile PTMs such as phosphorylation, glycosylation, or sulfonation. In these instances, the preferred reaction is often the cleavage of the PTM as opposed to the backbone of the peptide, resulting in a high intensity peak corresponding to the difference of the parent mass and the cleaved modification. The advent of electron capture dissociation (ECD) (10, 11) and electron transfer dissociation (ETD) (12–15) has enabled researchers to address the aforementioned issues associated with bottom up approaches using CID by adopting a complementary top down or middle down analysis strategy.ECD and ETD both involve the reaction of an electron with a highly protonated cation to form an odd electron peptide. This process induces large amounts of backbone cleavage to yield c and z· ions that are analogous to the b and y ion series typically encountered in CID tandem mass spectra. Unlike CID, ECD/ETD cleavage is weakly affected by the composition and number of amino acids in the peptide and for certain systems can provide more fragmentation coverage than CID alone, especially for bigger peptides with higher charge states. Both ECD and ETD also prevent the cleavage of labile modifications, and thus PTMs are retained on the corresponding c and z· ions. The aforementioned benefits make ECD/ETD particularly well suited for the LC-MS/MS top down and middle down analysis of post-translationally modified proteins. These top down and middle down approaches also enable the approximate inference of protein abundance from the chromatogram and MS¹ information because the full protein sequence elutes from the column (16).In recent years, there has been significant interest in the identification of highly modified proteins, such as histones. Histone proteins are key regulators of many important DNA processes in eukaryotes, and recent studies have elucidated complex relationships between histone modifications and many nuclear events. It has also been shown that differences in global histone modifications in tissues can be used to predict the clinical outcome of cancer patients (17). Early MS or immunoassay studies were only able to analyze these modifications on a site-by-site basis and as a result lost important connectivity information on the molecular level because several modified forms of the same protein exist concurrently. In MS-based applications, the use of traditional reversed phase HPLC for the separation of a highly modified protein results in poor chromatographic resolution because all the modified forms are physically similar. Successful off-line techniques for the separation of highly modified histone forms have been achieved using cation exchange hydrophilic interaction chromatography (HILIC) (18), which separates the modified species primarily by the number of acetyl groups and secondly by the degree of methylation. The separation must be conducted off line because the mobile phase additives used are non-volatile components, and subsequent fractionation is necessary for mass spectrometric analysis. This protocol has made it possible to analyze the first 50 amino acids of the N-terminal tail of histone H3 and provided important insight regarding connectivity information between the modification sites. A major disadvantage of this approach is that the off-line nature of the experimental protocol is extremely time-consuming (on the order of months) and thus prohibits the ability to conduct multiple runs for high throughput studies and statistical validation. Additionally, other off-line techniques have been successful in the extraction and purification of modified histone proteins using acid-urea gel electrophoresis (19) but suffer from similar throughput constraints.We have recently developed chromatography that is particularly suited for LC-MS ETD analysis of highly modified polypeptides with successful applications to histone proteins (20). The protocol uses a “saltless” pH gradient to elute the various modified forms in a weak cation exchange HILIC. Unprecedented separation of the modified histone forms is achieved within a single LC-MS/MS ETD experiment, thereby introducing important chromatographic information that can be utilized in the subsequent identification and quantification of these post-translational modifications. Although the achieved separation is exceptional in comparison with previous attempts, the complexity and relative similarity of the modified forms still results in minor species co-eluting with similar mass and retention times, thus resulting in multiplexed tandem mass spectra. The term “multiplexed” as used here refers to the fact that several species are dissociated and measured in a single tandem mass spectrum (21) and should not be confused with the multiplex experimental protocols. Computational methodologies that utilize the extensive and complementary information contained within these LC-MS/MS data sets are nonexistent as the technology has only recently been developed.In this work, we present a novel mixed integer linear optimization (MILP) computational framework for the identification and quantification of highly modified proteins using LC-MS and ETD tandem mass spectrometry. Key concepts of the proposed framework are illustrated using histone H3.2 as an example system. For a given primary sequence, the entire set of post-translational modifications that satisfy a precursor mass are enumerated by solving an MILP feasibility problem. Given this set of PTM forms, an MILP superposition problem is then solved to determine the relative fractions of the modified forms that are present in the multiplexed ETD tandem mass spectrum. An important aspect of the proposed framework is that chromatographic information is used to correlate the modification states as a function of modification position, mass, and time. The proposed computational framework is applied to an entire LC-MS/MS ETD experiment corresponding to a mixture of highly modified histone peptides to demonstrate its utility.     

Inferring the number of evolutionary events from DNA coding sequence differences

The estimation of the amount of evolutionary divergence that has taken place between two DNA coding sequences depends strongly on the degree of constraint on amino acid replacements. If amino acid replacements are relatively unconstrained, the individual nucleotide is the appropriate unit of analysis and the method of Tajima and Nei can be used. If amino acid replacements are constrained, however, this method is shown to be inapplicable. For sequences with strong amino acid constraints, a method is outlined analogous to the Tajima and Nei method using codons as the unit of analysis. Only synonymous substitutions are used. Codon usage data can be employed to estimate the necessary parameters of the calculation, or a priori models of substitution may be employed. Sequences with significant but intermediate constraints on amino acid replacements are, in principle, unanalyzable.      

Inflammatory thresholds and the species-specific effects of colonising bacteria in stable chronic obstructive pulmonary disease

Background

There has been increasing interest in the use of newer, culture-independent techniques to study the airway microbiome of COPD patients. We investigated the relationships between the three common potentially pathogenic microorganisms (PPMs) Haemophilus influenzae, Streptococcus pneumoniae and Moraxella catarrhalis, as detected by quantitative PCR (qPCR), and inflammation and health status in stable patients in the London COPD cohort.

Methods

We prospectively collected sputum, serum and plasma samples for analysis of airway bacterial presence and load, and airway and systemic inflammation from 99 stable COPD patients between January 2011 and October 2012. Health status was measured with St George’s Respiratory Questionnaire and COPD Assessment Test.

Results

Airway inflammation and plasma fibrinogen, but not C-reactive protein, were greater in samples with PPM detection (p < 0.001, p = 0.049 and p = 0.261, respectively). Increasing total bacterial load was associated with increasing airway (p < 0.01) but not systemic inflammation (p > 0.05). Samples with high total bacterial loads had significantly higher airway inflammation than both samples without PPM detection and those with lower loads. Haemophilus influenzae presence was associated with significantly higher levels of airway but not systemic inflammation for all given pathogen loads (p < 0.05), and was significantly greater than with other PPMs. No association was observed between inflammation and health status (p > 0.05).

Conclusions

Airway and systemic inflammation, as measured by fibrinogen, is greater in stable COPD patients with PPMs detected using the culture-independent qPCR technique. The airway, but not systemic inflammatory response, appears to have a total pathogen-load threshold and appears attributable to Haemophilus influenzae. However, discordance between inflammation and health status was observed.

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-014-0114-1) contains supplementary material, which is available to authorized users.     

Mitogenic activity of pituitary hormones on cell cultures of normal and carcinogen-induced tumor epithelium from rat mammary glands

Cell suspension containing normal or tumor epithelium were readily obtained by enzymatically digesting rat mammary glands from perphenazine-treated (prolactin-hypersecreting) cycling, female virgin animals or hormone- responsive mammary tumors from animal treated with dimethylbenzanthracene. Cell suspensions were fractioned into predominantly epithelial and predominantly stromal cells by their differential rates of attachment to culture dishes. Both normal mammary and tumor epithelial cells were characterized by the presence of specific cell-junctional complexes, desmosome-like structures, surface microvilli, and their ability to synthesize casein. Serum-dependent protease activity was greater in cultures derived from tumors, and cells from such cultures grew in agarose whereas those from the non-neoplastic gland did not. The addition of prolactin to the culture medium stimulated DNA synthesis in primary or secondary epithelial cultures from tumors, whereas additional insulin and hydrocortisone with prolactin were required for similar levels of DNA synthesis in cultures from non-neoplastic glands. The fraction of cells synthesizing DNA was, however, smaller than that with 10 percent serum measured in the same time period. Both growth hormone and epidermal growth factor stimulated DNA synthesis but to a lesser extent than did prolactin. Prolactin with hydrocortisone and insulin were relatively inactive in promoting DNA synthesis of the nonepithelial cells whereas pituitary fibroblast growth factor was more active. These mitogenic effects were obtained when the hormones were added to the medium at near physiological concentrations, and paralleled the known activities of the hormones in control of mammary gland growth and development in the rat.     

Characteristics of temporal patterns of cortisol and luteinizing hormone in primiparous,postpartum, anovular,suckled, beef cows exposed acutely to bulls

Background  

The physiological mechanism by which bulls stimulate resumption of ovarian cycling activity in postpartum, anovular, suckled cows after calving may involve the concurrent activation of the hypothalamic-hypophyseal-ovarian (HPO) axis and hypothalamic-hypophyseal-adrenal (HPA) axis. Thus, the objectives of this experiment were to determine if characteristics of temporal patterns of cortisol and luteinizing hormone (LH) in postpartum, anovular, beef cows are influenced by acute exposure to bulls. The null hypotheses were that daily, temporal characteristics of cortisol and LH concentration patterns do not differ between cows exposed acutely to bulls or steers.     

Reassembly of flagellar B (alpha beta) tubulin into singlet microtubules: consequences for cytoplasmic microtubule structure and assembly

B(alpha beta) tubulin was obtained from a homogeneous class of microtubules, the incomplete B subfiber of sea urchin sperm flagellar doublet microtubules, by thermal fractionation. The thermally derived soluble B tubulin fraction (100, 000 g-h) repolymerizes in vitro, yielding microtubule-like structures. The microtubule-associated protein (MAP) composition and certain assembly parameters of thermally derived B tubulin are different from those reported for sonication- derived flageller tubulin and purified vertebrate tubulin. The "microtubules" reassembled from thermally prepared B tubulin are composed of 12-15 protofilaments (73% possess 14 protofilaments). A certain number possess a single "adlumenal component" applied to their inside walls, regardless of the number of protofilaments. Following the first cycle of polymerization, 81% of the B tubulin and essentially 100% of the MAPs remain cold insoluble. Evidence suggests that B tubulin assembles faithfully into a B lattice, creating a j seam between two protofilaments that are laterally bonded in a A-lattice configuration. The significance of these seams is discussed in relation to the mechanism of microtubule assembly, the stability of observed ribbons of protofilaments, and the three-dimensional organization of microtubule-associated components.     

A tetravalent dengue nanoparticle stimulates antibody production in mice

Background

Dengue is a major public health problem worldwide, especially in the tropical and subtropical regions of the world. Infection with a single Dengue virus (DENV) serotype causes a mild, self-limiting febrile illness called dengue fever. However, a subset of patients experiencing secondary infection with a different serotype progresses to the severe form of the disease, dengue hemorrhagic fever/dengue shock syndrome. Currently, there are no licensed vaccines or antiviral drugs to prevent or treat dengue infections. Biodegradable nanoparticles coated with proteins represent a promising method for in vivo delivery of vaccines.

Findings

Here, we used a murine model to evaluate the IgG production after administration of inactivated DENV corresponding to all four serotypes adsorbed to bovine serum albumin nanoparticles. This formulation induced a production of anti-DENV IgG antibodies (p < 0.001). However, plaque reduction neutralization assays with the four DENV serotypes revealed that these antibodies have no neutralizing activity in the dilutions tested.

Conclusions

Our results show that while the nanoparticle system induces humoral responses against DENV, further investigation with different DENV antigens will be required to improve immunogenicity, epitope specicity, and functional activity to make this platform a viable option for DENV vaccines.