The antiphospholipid syndrome is defined by the presence of antiphospholipid antibodies in blood of patients with thrombosis or fetal loss. There is ample evidence that ␤ 2 -glycoprotein I (␤ 2 GPI) is the major antigen for antiphospholipid antibodies. The autoantibodies recognize ␤ 2 GPI when bound to anionic surfaces and not in solution. We showed that ␤ 2 GPI can exist in at least 2 different conformations: a circular plasma conformation and an "activated" open conformation. We also showed that the closed, circular conformation is maintained by interaction between the first and fifth domain of ␤ 2 GPI. By changing pH and salt concentration, we were able to convert the conformation of ␤ IntroductionThe antiphospholipid syndrome (APS) is defined as the presence of antiphospholipid antibodies in the blood of patients with thrombosis or fetal loss. The APS is one of the most common causes of acquired thrombophilia, 1 especially at younger age. In 1990, it was shown that the so-called antiphospholipid antibodies do not recognize phospholipids directly but they interact with phospholipids via the plasma protein ␤ 2 -glycoprotein I (␤ 2 GPI). [2][3][4] However, the discovery of ␤ 2 GPI as target for the autoantibodies did not provide a more in-depth knowledge on the underlying cause of the syndrome. It was unclear which metabolic pathway was disturbed by the autoantibodies because no physiologic function has convincingly been ascribed to ␤ 2 GPI to date. Nevertheless, as antibodies against ␤ 2 GPI can induce thrombosis in animal models, 5-7 the protein ␤ 2 GPI must hold an important functional clue to our understanding of the syndrome.␤ 2 GPI is a highly abundant 43-kDa protein that circulates at a concentration of approximately 200 g/mL. ␤ 2 GPI consists of 326 amino acids arranged in 5 short consensus repeat domains. 8,9 The first 4 domains contain 60 amino acids each, whereas the fifth domain has a 6-residue insertion and an additional 19-amino acid C-terminal extension. The extra amino acids are responsible for the formation of a large positively charged patch within the fifth domain of ␤ 2 GPI 10 that forms the binding site for anionic phospholipids. The anti-␤ 2 GPI antibodies that recognize an epitope located in the first domain correlate better with the thrombotic complications than antibodies directed against other domains. 11-13 Antibodies directed against ␤ 2 GPI have become one of the serologic markers characterizing the APS. 14 After binding to anionic surfaces, ␤ 2 GPI exposes a cryptic epitope that is recognized by the autoantibodies present in the APS. 11,12,15,16 These antibodies only recognize ␤ 2 GPI when it is bound to a surface and do not recognize ␤ 2 GPI in solution. Moreover, no circulating immune complexes between antibodies and ␤ 2 GPI have been detected in patient plasmas. 17 This seems not to be the result of clearance of these complexes from plasma because plasma levels of ␤ 2 GPI in antiphospholipid patients are the same as plasma levels of ␤ 2 GPI in healthy persons. 18 The crystal st...

The peroxisomal protein import receptor Pex5p is modified by ubiquitin, both in an Ubc4p-dependent and -independent manner. Here we show that the two types of ubiquitination target different residues in the NH 2 -terminal region of Pex5p and we identify Pex4p (Ubc10p) as the ubiquitin-conjugating enzyme required for Ubc4p-independent ubiquitination. Whereas Ubc4p-dependent ubiquitination occurs on two lysine residues, Pex4p-dependent ubiquitination neither requires lysine residues nor the NH 2 -terminal ␣-NH 2 group. Instead, a conserved cysteine residue appears to be essential for both the Pex4p-dependent ubiquitination and the overall function of Pex5p. In addition, we show that this form of ubiquitinated Pex5p is susceptible to the reducing agent ␤-mercaptoethanol, a compound that is unable to break ubiquitin-NH 2 group linkages. Together, our results strongly suggest that Pex4p-dependent ubiquitination of Pex5p occurs on a cysteine residue.

The majority of mass spectrometry-based protein quantification studies uses peptide-centric analytical methods and thus strongly relies on efficient and unbiased protein digestion protocols for sample preparation. We present a novel objective approach to assess protein digestion efficiency using a combination of qualitative and quantitative liquid chromatography-tandem MS methods and statistical data analysis. In contrast to previous studies we employed both standard qualitative as well as data-independent quantitative workflows to systematically assess trypsin digestion efficiency and bias using mitochondrial protein fractions. We evaluated nine trypsin-based digestion protocols, based on standard in-solution or on spin filter-aided digestion, including new optimized protocols. We investigated various reagents for protein solubilization and denaturation (dodecyl sulfate, deoxycholate, urea), several trypsin digestion conditions (buffer, RapiGest, deoxycholate, urea), and two methods for removal of detergents before analysis of peptides (acid precipitation or phase separation with ethyl acetate). Our data-independent quantitative liquid chromatography-tandem MS workflow quantified over 3700 distinct peptides with 96% completeness between all protocols and replicates, with an average 40% protein sequence coverage and an average of 11 MS-based proteomics is an indispensable technology for the characterization of complex biological systems, including relative or absolute protein expression levels and protein post-translational modifications. The most popular method for analyzing medium to high complexity protein samples in large-scale proteomics relies on protein digestion by using the endoprotease trypsin. Analysis and sequencing of tryptic peptides by liquid chromatography-tandem MS (LC-MS/MS) 1 then enables identification and determination of protein expression levels based on the peptide ion abundance level or the (fragment) ion intensities of identified peptides. This peptide-centric approach thus strongly relies on efficient, unbiased and reproducible protein digestion protocols. Efficiency is required to maximize the number of detectable peptides per protein (coverage) to distinguish unique proteins within protein families with similar sequences and/or sequence variants, and to detect post-translational modifications. Unbiased generation of peptides is required for the resulting data set to most accurately reflect the relative (stoichiometry) and absolute protein abundance in a sample. A particular protocol should be unbiased with respect to abundance, molecular weight, hydrophobicity and protein class. Membrane proteins for example are often suspected to be underrepresented. For MS-based proteomics approaches several critical steps can be distinguished: (a) disruption and solubilization of cells and protein complexes, (b) protein denaturation and enzymatic proteolysis, (c) MS-compatible peptide recovery, which normally entails removal of reagent leftovers and desalting before MS analysis, (d) adequate pept...

SignificanceCircumstantial evidence indicates that especially deep-ocean heterotrophic microbes rely on particulate organic matter sinking through the oceanic water column and being solubilized to dissolved organic matter (DOM) prior to utilization rather than on direct uptake of the vast pool of DOM in the deep ocean. Comparative metaproteomics allowed us to elucidate the vertical distribution and abundance of microbially mediated transport processes and thus the uptake of solutes throughout the oceanic water column. Taken together, our data suggest that, while the phylogenetic composition of the microbial community is depth stratified, the composition and substrate specificities of transporters considered in this study are ubiquitous while their relative abundance changes with depth.

Elucidating how and to what extent lipid metabolism is remodeled under changing conditions is essential for understanding cellular physiology. Here, we analyzed proteome and lipidome dynamics to investigate how regulation of lipid metabolism at the global scale supports remodeling of cellular architecture and processes during physiological adaptations in yeast. Our results reveal that activation of cardiolipin synthesis and remodeling supports mitochondrial biogenesis in the transition from fermentative to respiratory metabolism, that down-regulation of de novo sterol synthesis machinery prompts differential turnover of lipid droplet-associated triacylglycerols and sterol esters during respiratory growth, that sphingolipid metabolism is regulated in a previously unrecognized growth stage-specific manner, and that endogenous synthesis of unsaturated fatty acids constitutes an in vivo upstream activator of peroxisomal biogenesis, via the heterodimeric Oaf1/Pip2 transcription factor. Our work demonstrates the pivotal role of lipid metabolism in adaptive processes and provides a resource to investigate its regulation at the cellular level.

Macroscopic growths at geographically separated acid mine drainages (AMDs) exhibit distinct populations. Yet, local heterogeneities are poorly understood. To gain novel mechanistic insights into this, we used OMICs tools to profile microbial populations coexisting in a single pyrite gallery AMD (pH ∼2) in three distinct compartments: two from a stratified streamer (uppermost oxic and lowermost anoxic sediment-attached strata) and one from a submerged anoxic non-stratified mat biofilm. The communities colonising pyrite and those in the mature formations appear to be populated by the greatest diversity of bacteria and archaea (including ‘ARMAN' (archaeal Richmond Mine acidophilic nano-organisms)-related), as compared with the known AMD, with ∼44.9% unclassified sequences. We propose that the thick polymeric matrix may provide a safety shield against the prevailing extreme condition and also a massive carbon source, enabling non-typical acidophiles to develop more easily. Only 1 of 39 species were shared, suggesting a high metabolic heterogeneity in local microenvironments, defined by the O2 concentration, spatial location and biofilm architecture. The suboxic mats, compositionally most similar to each other, are more diverse and active for S, CO2, CH4, fatty acid and lipopolysaccharide metabolism. The oxic stratum of the streamer, displaying a higher diversity of the so-called ‘ARMAN'-related Euryarchaeota, shows a higher expression level of proteins involved in signal transduction, cell growth and N, H2, Fe, aromatic amino acids, sphingolipid and peptidoglycan metabolism. Our study is the first to highlight profound taxonomic and functional shifts in single AMD formations, as well as new microbial species and the importance of H2 in acidic suboxic macroscopic growths.

Post-translational modifications (PTMs) of histones play a major role in regulating chromatin dynamics and influence processes such as transcription and DNA replication. Here, we report 114 distinct combinations of coexisting PTMs of histone H3 obtained from mouse embryonic stem (ES) cells. Histone H3 N-terminal tail peptides (amino acids 1-50, 5-6 kDa) were separated by optimized weak cation exchange/hydrophilic interaction liquid chromatography (WCX/HILIC) and sequenced online by electron transfer dissociation (ETD) tandem mass spectrometry (MS/MS). High mass accuracy and near complete sequence coverage allowed unambiguous mapping of the major histone marks and discrimination between isobaric and nearly isobaric PTMs such as trimethylation and acetylation. Hierarchical data analysis identified H3K27me2-H3K36me2 as the most frequently observed PTMs in H3. Modifications at H3 residues K27 and K36 often coexist with the abundant mark K23ac, and we identified two frequently occurring quadruplet marks 'K9me1K23acK27me2K36me2' and 'K9me3K23acK27me2K36me', which might indicate a role in crosstalk. Co-occurrence frequency analysis revealed also an interplay between methylations of K9, K27, and K36, suggesting interdependence between histone methylation marks. We hypothesize that the most abundant coexisting PTMs may provide a signature for the permissive state of mouse ES cells.

The human endothelial cell plasma membrane harbors two subdomains of similar lipid composition, caveolae and rafts, both crucially involved in various essential cellular processes like transcytosis, signal transduction and cholesterol homeostasis. Caveolin-enriched membranes, isolated by either cationic silica or buoyant density methods, were explored by comparing large series of two-dimensional (2-D) maps and subsequent identification of over 100 protein spots by matrix-assisted laser desorption/ionization (MALDI) peptide mass fingerprinting. Improved representation and identification of membrane proteins and valuable information on various post-translational modifications was achieved by the presented optimized procedures for solubilization, destaining and database searching/computing. Whereas the cationic silica purification yielded predominantly known endoplasmic reticulum residents, the cold-detergent method yielded a large number of known caveolae residents, including caveolin-1. Thus, a large part of this subproteome was established, including known (trans-)membrane, signal transduction and glycosyl phosphatidylinositol (GPI)-anchored proteins. Several predicted proteins from the human genome were isolated for the first time from biological samples, including SGRP58, SLP-2, C8ORF2, and XRP-2. These findings and various optimized procedures can serve as a reference to study the differential composition of endothelial cell caveolae and rafts, known to be involved in pathologies like cancer and cardiovascular disease.