Asparagine deamidation perturbs antigen presentation on class II major histocompatibility complex molecules

3-phosphoinositide-dependent kinase 1 deficiency perturbs Toll-like receptor signaling events and actin cytoskeleton dynamics in dendritic cells

The adaptive immune response depends on dendritic cell (DC) activation by microbial products that signal via pattern recognition receptors and activate mitogen-activated protein kinases, NFkappaB and PI3K. The contribution of the AGC kinase family, including protein kinase B, protein kinase C, p90kDa ribosomal S6 kinase, and S6 kinase, has been little investigated because the probable redundancy among their isoforms makes their study difficult. We took advantage of the fact that all these kinases are regulated by the upstream master kinase 3-phosphoinositide-dependent kinase 1 (PDK1). Here we analyze various properties of DC from mice expressing approximately 10% of normal PDK1 (PDK1(fl/-)). DC populations in lymphoid and nonlymphoid tissues appeared normal in PDK1(fl/-) mice, and some in vitro responses to lipopolysaccharide (LPS) such as cytokine production were normal in cultured bone marrow DC. However, LPS-induced expression of class II major histocompatibility complex and CD86 were elevated in PDK1(fl/-) BMDC and PDK1(fl/-) spleen DC produced more interleukin-10 and -12, implying an attenuating role for PDK1. Unexpectedly, PDK1(fl/-) DC had a significantly reduced capacity for LPS-stimulated macropinocytosis and phagocytosis that correlated with a lowered F-actin/G-actin ratio, apparently because of increased actin depolymerization. Several PDK1-regulated kinases, some of which feed into actin regulators, showed reduced activation in PDK1(fl/-) DC. Reintroduction of PDK1 restored S6 kinase activity, increased levels of F-actin, and boosted macropinocytosis thus linking PDK1 and its downstream effectors to the unusual phenotype of PDK1(fl/-) DC.

DNA damage-induced Bcl-xL deamidation is mediated by NHE-1 antiport regulated intracellular pH

The pro-survival protein Bcl-x_L is critical for the resistance of tumour cells to DNA damage. We have previously demonstrated, using a mouse cancer model, that oncogenic tyrosine kinase inhibition of DNA damage–induced Bcl-x_L deamidation tightly correlates with T cell transformation in vivo, although the pathway to Bcl-x_L deamidation remains unknown and its functional consequences unclear. We show here that rBcl-x_L deamidation generates an iso-Asp⁵²/iso-Asp⁶⁶ species that is unable to sequester pro-apoptotic BH3-only proteins such as Bim and Puma. DNA damage in thymocytes results in increased expression of the NHE-1 Na/H antiport, an event both necessary and sufficient for subsequent intracellular alkalinisation, Bcl-x_L deamidation, and apoptosis. In murine thymocytes and tumour cells expressing an oncogenic tyrosine kinase, this DNA damage–induced cascade is blocked. Enforced intracellular alkalinisation mimics the effects of DNA damage in murine tumour cells and human B-lineage chronic lymphocytic leukaemia cells, thereby causing Bcl-x_L deamidation and increased apoptosis. Our results define a signalling pathway leading from DNA damage to up-regulation of the NHE-1 antiport, to intracellular alkalanisation to Bcl-x_L deamidation, to apoptosis, representing the first example, to our knowledge, of how deamidation of internal asparagine residues can be regulated in a protein in vivo. Our findings also suggest novel approaches to cancer therapy.

Cell survival and cell death (apoptosis) are controlled by a finely tuned ensemble of pro-survival and pro-apoptotic proteins. When the two types of protein are balanced, cells survive. But if the pro-survival proteins dominate, there is a danger that cells with damaged DNA will stay alive, leading to malignancy. One of the key pro-survival proteins, Bcl-x_L, acts by blocking the actions of pro-apoptotic proteins. We show here that DNA damage results in an important modification of Bcl-x_L. Specifically, when the amide groups are removed from two critical asparagine (amino acid) residues, Bcl-x_L can no longer block pro-apoptotic proteins, leading to cell death. Surprisingly, Bcl-x_L deamidation is catalysed not by an enzyme, but by increased pH inside the cell due to the up-regulation of an NHE-1 transporter that moves positive ions across the cell membrane. Indeed, artificially increasing pH causes Bcl-x_L deamidation and apoptosis in the absence of initial DNA damage. Exploring this novel pathway may ultimately suggest approaches to cancer therapy, especially when malignant cells are resistant to chemotherapy or radiotherapy.

Until now, the mechanisms and functional implications for DNA damage-induced Bcl-x_L deamidation were unknown. Here the authors provide important new insights into this phenomenon and its impact on cell survival.

Multiple asparagine deamidation of Bacillus anthracis protective antigen causes charge isoforms whose complexity correlates with reduced biological activity

Protective antigen is essential for the pathology of Bacillus anthracis and is the proposed immunogen for an improved human anthrax vaccine. Known since discovery to comprise differentially charged isoforms, the cause of heterogeneity has eluded specific structural definition until now. Recombinant protective antigen (rPA) contains similar isoforms that appear early in fermentation and are mostly removed through purification. By liquid chromatography-tandem mass spectrometry sequencing of the entire protein and inspection of spectral data for amino acid modifications, pharmaceutical rPA contained measurable deamidation at seven of its 68 asparagine residues. A direct association between isoform complexity and percent deamidation was observed such that each decreased with purity and increased with protein aging. Position N537 consistently showed the highest level of modification, although its predicted rate of deamidation ranked 10th by theoretical calculation, and other asparagines of higher predicted rates were observed to be unmodified. rPA with more isoforms and greater deamidation displayed lower activities for furin cleavage, heptamerization, and holotoxin formation. Lethal factor-mediated macrophage toxicity correlated inversely with deamidation at residues N466 and N408. The described method measures deamidation without employing theoretical isotopic distributions, comparison between differentially treated samples or computational predictions of reactivity rates, and is broadly applicable to the characterization of other deamidated proteins.

Gastrokine 1 expression in patients with and without Helicobacter pylori infection

BACKGROUND

To understand the molecular changes underlying Helicobacter pylori-related gastric diseases is mandatory to prevent gastric cancer. Proteomic technology is providing a rapid expansion of the basic knowledge, particularly in the discovery of new biomarkers involved in the tumourigenesis.

AIM

To characterise changes in protein expression level of the gastric mucosa in H. pylori-infected patients.

METHODS

The population enrolled comprised 41 dyspeptic patients. Proteins extracted from gastric mucosal specimens were analysed by 2-dimensional electrophoresis, sequenced by MALDI-TOF and identified by Edman's degradation.

RESULTS

Twenty-one out of 41 patients had H. pylori infection of whom 17 had anti-CagA IgG antibodies. Several proteins were identified, of which Rho guanosine diphosphatase dissociation inhibitor alpha and heat shock protein 27 increased and glutathione transferase and antrum mucosa protein-18 decreased in H. pylori-positive in respect to H. pylori-negative patients. Interestingly, antrum mucosa protein-18, currently referred as gastrokine-1, showed two isoforms differing in the first N-terminal amino acid residue. Both gastrokine-1 isoforms were observed in the H. pylori-negative group whereas a lower expression or even absence of the gastrokine-1 basic isoform was found in a subgroup (7/21) of H. pylori-positive patients with moderate-severe gastritis.

CONCLUSION

Our study demonstrated the presence of gastrokine-1 isoforms of which the basic isoform was reduced in a subset of patients with H. pylori infection.

A modified peptide mapping strategy for quantifying site-specific deamidation by electrospray time-of-flight mass spectrometry

A modified peptide mapping strategy using electrospray time-of-flight mass spectrometry with high-performance liquid chromatography (HPLC/MS) provides an improved measure of deamidation by performing proteolytic digestion at low temperature (4 degrees C), low pH (6.0) and in organic solvent (> or =10% acetonitrile). HPLC resolution of the native (N) and deamidated (D) peptides is achieved, and the ratio of ion counts is converted into percent deamidation. The percent deamidation is established for a reference lot using a time course of digestion (24-120 h) and extrapolation to time zero. Test samples are compared against the reference lot to quantitate changes in site-specific deamidation. A recombinant purified protein (antigen A) having a single labile Asn-Gly site is analyzed using this strategy. The N and D peptides from an endoproteinase Lys C (Lys C) digestion (pH 6, 4 degrees C) resolve to near homogeneity on HPLC which results in equivalent percent deamidation when calculated by either UV or ion counts. Deamidation increases with time and pH of proteolysis. Lys C peptide maps of antigen A and bovine serum albumin (BSA) digested at pH 5-8 are comparable. A Lys C digestion time course of a reference lot of antigen A extrapolates to 18% deamidation of the Asn-Gly site at time zero. This strategy may be generally applicable to protease-protein combinations for improved accuracy in measuring site-specific deamidation by peptide mapping LC/MS.

Biochemistry of amino acid racemization and clinical application to musculoskeletal disease

During aging, proteins are subject to numerous forms of damage. Several types of non-enzymatic post-translational modifications have been described in aging proteins, including oxidation, nitration, glycation, and racemization. Racemization of amino acids is the spontaneous conversion of L-enantiomers to the D-form, which is dependent on temperature, pH, and time. Because of the time-dependent nature of racemization, it can be used to determine the relative age and turnover rates of long-lived proteins. There are many such long-lived proteins within the body; they are found in the brain, eye, and heart, but are particularly abundant in proteins found in musculoskeletal tissues such as bone and cartilage. During disease, musculoskeletal tissues have pathologically altered turnover rates. Because turnover rates can be estimated from levels of racemization, racemized musculoskeletal protein fragments may serve as useful biomarkers of disease. This review discusses the biochemistry of amino acid racemization in proteins and its clinical application to musculoskeletal disease.

Post-translational modifications of naturally processed MHC-binding epitopes

A variety of different post-translational modifications of peptides displayed by class I and II MHC molecules have now been described. Some modifications promote the binding of peptides to MHC molecules, and might also influence the ability of the peptide to be produced by antigen processing pathways. In some instances, the antigen processing components themselves are actually responsible for generating post-translational modifications. Finally, evidence is accumulating that modifications can be altered as a consequence of inflammation, transformation, apoptosis and aging. This leads to altered repertories of MHC-associated peptides, which may be important in immune responses associated with autoimmune diseases, infection and cancer.

Effects of Spontaneous Deamidation on the Cytotoxic Activity of the Bacillus anthracis Protective Antigen

Protective antigen (PA) is a central virulence factor of Bacillus anthracis and a key component in anthrax vaccines. PA binds to target cell receptors, is cleaved by the furin protease, self-aggregates to heptamers, and finally internalizes as a complex with either lethal or edema factors. Under mild room temperature storage conditions, PA cytotoxicity decreased (t(1/2) approximately 7 days) concomitant with the generation of new acidic isoforms, probably through deamidation of Asn residues. Ranking all 68 Asn residues in PA based on their predicted deamidation rates revealed five residues with half-lives of <60 days, and these residues were further analyzed: Asn10 in the 20-kDa region, Asn162 at P6 vicinal to the furin cleavage site, Asn306 in the pro-pore translocation loop, and both Asn713 and Asn719 in the receptor-binding domain. We found that PA underwent spontaneous deamidation at Asn162 upon storage concomitant with decreased susceptibility to furin. A panel of model synthetic furin substrates was used to demonstrate that Asn162 deamidation led to a 20-fold decrease in the bimolecular rate constant (k(cat)/Km) of proteolysis due to the new negatively charged residue at P6 in the furin recognition sequence. Furthermore, reduced PA cytotoxicity correlated with a decrease in PA cell binding and also with deamidation of Asn713 and Asn719. On the other hand, neither deamidation of Asn10 or Asn306 nor impairment of heptamerization could be observed upon prolonged PA storage. We suggest that PA inactivation during storage is associated with susceptible deamidation sites, which are intimately involved in both mechanisms of PA cleavage by furin and PA-receptor binding.

Asparaginyl endopeptidase: case history of a class II MHC compartment protease

Although the endpoint of the class II antigen-processing pathway is well characterized, the processing events that lead to the production of class II major histocompatibility complex (MHC)/peptide complexes are not. It is generally assumed that protease action on native antigen substrates leads to unfolding and capture of either long or short peptides. Whether specific protease activities are needed for presentation of particular T-cell epitopes is largely unknown. Here, we review our recent studies that aim to identify the processing enzymes that initiate processing of different antigens. We suggest a general strategy that can potentially identify preferred relationships between substrates and processing enzymes in vitro and suggest ways in which these relationships can be tested in vivo. We draw heavily on the example of asparaginyl endopeptidase, which is involved in both productive and destructive processing of different antigen substrates. Overall, while there is undoubtedly redundancy in class II MHC antigen processing, the contributions of individual enzymes can be clearly dissected.