A tale of two oxidation states: bacterial colonization of arsenic-rich environments.

Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments-including ground and surface waters-from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the beta-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth.

Structural study of Carcinus maenas hemocyanin by native ESI-MS: interaction with L-lactate and divalent cations.

The interaction of L-lactate and divalent cations with Carcinus maenas hemocyanin has been probed by electrospray ionization mass spectrometry under conditions preserving noncovalent interactions (native ESI-MS). C. maenas native hemocyanin in the hemolymph occurs mainly as dodecamers and to a lesser extent as hexamers. A progressive acidification with formic acid after alkaline dissociation resulted in the preferential recruitment of the two lightest subunits into light dodecamers, a molecular complex absent from native hemolymph, in addition to regular dodecamers and hexamers. Addition of L-lactic acid also induced the recruitment of these subunits, even at alkaline pH. A dodecamer-specific subunit is needed to enable aggregation over the hexameric state. Experiments with EDTA suggested the existence of different binding sites and association constants for divalent cations within hexameric structures and at the interface between two hexamers. L-lactic acid specific interaction with the lightest subunits was not inhibited by removal of the divalent cations.

The structural analysis of large noncovalent oxygen binding proteins by MALLS and ESI-MS: a review on annelid hexagonal bilayer hemoglobin and crustacean hemocyanin.

Understanding the function of macromolecular complexes is related to a precise knowledge of their structure. These large complexes are often fragile high molecular mass noncovalent multimeric proteins. Classical biochemical methods for determination of their native mass and subunit composition were used to resolve their quaternary structure, sometimes leading to different models. Recently, the development of mass spectrometry and multi-angle laser light scattering (MALLS) has enabled absolute determination of native masses and subunit masses. Electrospray ionization mass spectrometry (ESI-MS) was used in denaturing and native conditions to probe subunit composition and noncovalent assemblies masses up to 2.25 MDa. In a complementary way, MALLS provides mass and size estimation in various aqueous solvents. ESI-MS method can also give insights into post-translational modifications (glycosylation, disulfide bridges ). By combining native mass and subunit composition data, structural models can be proposed for large edifices such as annelid extracellular hexagonal bilayer hemoglobins (HBL Hb) and crustacean hemocyanins (Hc). Association/dissociation mechanisms, protein-protein interactions, structural diversity among species and environmental adaptations can also be addressed with these methods. With their absolute mass determination, the very high precision of spectrometry and the versatile nature of light scattering, ESI-MS and MALLS have provided a wealth of data helping to resolve parts of controversies for HBL-Hb models and opening access to new fields of investigation in structural diversity and molecular adaptation. In this review we will focus on annelid HBL-Hb and on crustacean Hc and on the original contributions of ESI-MS and MALLS in this field.

Comparative ESI-MS study of approximately 2.2 MDa native hemocyanins from deep-sea and shore crabs: from protein oligomeric state to biotope.

In the past years, the potential of electrospray ionization mass spectrometry (ESI-MS) for the observation of intact weak interactions, such as non-covalent protein-ligand, protein-protein, protein-DNA complexes, has spread out. The coupling of ESI with time-of-flight (TOF) and quadrupole-time-of-flight (Q-TOF) analyzers has even enabled the detection of larger complexes with molecular weights greatly higher than 200 kDa. In this paper, we report a comparative ESI-MS study on the protein quaternary structure of native hemocyanins (Hc) from crabs living in different biotopes: a shore crab (Carcinus maenas) and two deep-sea crabs (Segonzacia mesatlantica and Bythograea thermydron). Hc is an extracellular blood protein, composed of several protein chains which can associate in large multimers. The goal of this study is to point out that the oligomerization state of native Hcs is biotope-dependent. Depending on the crab, ESI-MS analyses under non-denaturing conditions reveal different oligomeric forms present in equilibrium in solution. Molecular weights up to 2,235 kDa were measured for the associations of 30 subunits of the Bythograea thermydron Hc. Thanks to ESI-MS analyses, it could be concluded for the first time that the oligomerization state of native Hcs is dependent on the crab environment. The investigation of these different non-covalent self-assemblies is very important for the life history of crabs, since they are directly related with different oxygen binding abilities and thus, with their ability to colonize habitats with different oxygen contents.

Characterization of multimetallic grid-type complexes by electrospray mass spectrometry.

The self-assembly of the terdentate ligands 1a-h, based on terpyridine-like binding sites, with octahedrally coordinated metal ions, such as Fe(II), Co(II), Cu(II), Zn(II), Cd(II), Hg(II) and Pb(II), leads to the formation of the supramolecular grid-type complexes 2a-c(M(II)), 3d-g(M(II)) and 4h(M(II)). The structures and compositions of these coordination complexes in solution were deduced from electrospray mass spectrometry (ESMS) measurements. The results agree with the data available from x-ray radiocrystallography in the solid state and/or NMR spectroscopy in solution. ESMS may be applied in cases where other methods are difficult to use or inconclusive. This study stresses the power of ESMS in supramolecular chemistry.

Respiratory adaptations to the deep-sea hydrothermal vent environment: the case of Segonzacia mesatlantica, a crab from the Mid-Atlantic Ridge.

Segonzacia mesatlantica (Crustacea; Decapoda; Brachyura) is the only endemic crab species known from the Mid-Atlantic Ridge (MAR) hydrothermal vents. Known from all explored sites in the Atlantic, its wide distribution makes this species a model to study physiological adaptation, and specifically respiratory strategies. Native haemocyanin (Hc) comprises four non-covalent associations in equilibrium formed by monomers, hexamers, dodecamers and octadecamers made up of approximately 75 kDa polypeptide chains. Four different amino acid chains are observed with a molecular mass ranging from 75,234 to 75,972 Da. Experiments carried-out under pressure suggested that the percentage of monomer increased in the haemolymph under hypoxic condition. We have also observed a shift of the proportion of the two dodecamer series, suggesting a rapid modification of the Hc phenotype between hypoxic and hyperoxic conditions. Native Hc possesses a high oxygen affinity ( P50 = 2.2 Torr at 15 degrees C and pH 7.5), a large Bohr effect (Deltalog P50 / DeltapH approximately -2.7) and a slightly reverse temperature effect (DeltaH = +17.19 kJ mol(-1). The composition of Segonzacia haemolymph is similar to that of other littoral species except for the large enrichment in free copper and zinc. As for other species from hydrothermal vent sites, Segonzacia haemolymph possesses a higher buffer capacity than littoral species. Moreover, species from the hydrothermal vent decapods from Pacific hydrothermal vent that encounter higher CO2 content in their environment have a higher buffer capacity than Atlantic vent species. The results presented are discussed in relation with the physico-chemical characteristics of the hydrothermal vent environment.

Kinetic and Thermodynamic Control in Self-Assembly: Sequential Formation of Linear and Circular Helicates.

NMR and MS analysis as a function of time has shown that the self-assembly of a linear ligand with Fe2+ or Ni2+ , metal ions of octahedral coordination geometry, generates first a triple helicate and thereafter the circular helicate 1 as kinetic and thermodynamic products, respectively. The results provide insight into features of the energy hypersurface on which this self-assembly operates and point to the general role of kinetic and thermodynamic control in such processes.

Released selective pressure on a structural domain gives new insights on the functional relaxation of mitochondrial aspartyl-tRNA synthetase.

Mammalian mitochondrial aminoacyl-tRNA synthetases are nuclear-encoded enzymes that are essential for mitochondrial protein synthesis. Due to an endosymbiotic origin of the mitochondria, many of them share structural domains with homologous bacterial enzymes of same specificity. This is also the case for human mitochondrial aspartyl-tRNA synthetase (AspRS) that shares the so-called bacterial insertion domain with bacterial homologs. The function of this domain in the mitochondrial proteins is unclear. Here, we show by bioinformatic analyses that the sequences coding for the bacterial insertion domain are less conserved in opisthokont and protist than in bacteria and viridiplantae. The divergence suggests a loss of evolutionary pressure on this domain for non-plant mitochondrial AspRSs. This discovery is further connected with the herein described occurrence of alternatively spliced transcripts of the mRNAs coding for some mammalian mitochondrial AspRSs. Interestingly, the spliced transcripts alternately lack one of the four exons that code for the bacterial insertion domain. Although we showed that the human alternative transcript is present in all tested tissues; co-exists with the full-length form, possesses 5'- and 3'-UTRs, a poly-A tail and is bound to polysomes, we were unable to detect the corresponding protein. The relaxed selective pressure combined with the occurrence of alternative splicing, involving a single structural sub-domain, favors the hypothesis of the loss of function of this domain for AspRSs of mitochondrial location. This evolutionary divergence is in line with other characteristics, established for the human mt-AspRS, that indicate a functional relaxation of non-viridiplantae mt-AspRSs when compared to bacterial and plant ones, despite their common ancestry.

Lanthanide complexation with CMPO and CMPO-calix[4]arenes in solution: spectrophotometric and electrospray mass spectrometric approaches.

The binding of lanthanide(III) cations with organophosphorous ligands like CMPO and related calix[4]arene-based derivatives have been investigated using two experimental methods. The stability constants of the lanthanum, europium and ytterbium complexes were first determined in methanol by UV absorption spectrophotometry in the presence of nitrate or chloride anions. The results showed that the stoichiometry and the stability of the complexes formed depend on the position of the CMPO moieties either on the wide or the narrow rim of the calixarene scaffold, the nature of the medium, the conformational mobility of the ligands. Complexation of lanthanum was also followed by ESI-mass spectrometry in the same solvent. This method confirmed the stoichiometry of the complexes, giving also structural information, like coordination of anion or solvent molecules to the complexes, and allowed the calculation of distribution curves in good agreement with those derived from the spectrophotometric results. This is an important result showing that ESI-MS can be used to provide with quantitative information when absorption spectrophotometry is not applicable, i.e. for systems where complexation leads to weak spectral changes.

Analysis of aldosterone-induced differential receptor-independent protein patterns using 2D-electrophoresis and mass spectrometry.

In the human body the mineralocorticoid aldosterone is responsible for maintaining water and electrolyte homeostasis and therefore controlling blood pressure. In addition, aldosterone has recently been associated with severe heart failure. Besides receptor-dependent action, the damaging effects of aldosterone may also be partly mediated through non-genomic mechanisms. The present study focuses on the mineralocorticoid receptor-independent action of aldosterone at the protein level. We chose the fission yeast Schizosaccharomyces pombe as a model organism, since this yeast does not contain nuclear steroid receptors, but many genes and regulatory mechanisms that are close to those of mammals. Using 2D-electrophoresis we identified for the first time protein spots affected by aldosterone in a nuclear receptor-free system. Mass spectrometry analysis using MALDI-TOF MS and nanoLC-MS/MS approaches allowed the unambiguous identification of 11 proteins that showed increased or decreased levels, which may represent newly identified players and pathways of aldosterone-induced action. Two proteins with a connection to osmotic regulation (NAD-dependent malic enzyme and glycerol-3-phosphate-dehydrogenase), as well as two proteins involved in the overall organization of the cytoskeleton, vip1 and glyceraldehyde-3-phosphate dehydrogenase, which was also found to be specifically affected by aldosterone in human HCT116 cells, are discussed.

Electrospray mass spectrometry analysis of dendritic branches bearing peripheral fullerene subunits.

The electrospray mass spectrometric characterization of neutral dendrons with a carboxylic acid function or a t-butyl ester moiety at the central point and up to eight peripheral C60 subunits has been performed and is described in detail. Molecules bearing a carboxylic acid group at the center turned out to be preferentially ionized by deprotonation, whereas those with a t-butyl ester head group were ionized by reduction of the C60 units in the infusion capillary of the electrospray source.

Proteome analysis of Schizosaccharomyces pombe by two-dimensional gel electrophoresis and mass spectrometry.

The fission yeast Schizosaccharomyces pombe (S. pombe) is a unicellular eukaryote and contains many genes and regulatory mechanisms that are close to those of mammals. In this study, we performed a global proteomic analysis of the fission yeast S. pombe wild type h(-S) L 972 proteome. More than 1,500 protein spots were visualized on silver stained 2-D gels in the 3-10 pI range with a high resolution and high reproducibility. Protein identification was carried out by MALDI-TOF-MS and/or nanoLC-MS/MS. Advantage of the complementarity of these two MS approaches was used to enhance the identification quality. So far, 364 proteins (representing 157 different proteins) have been identified. We report here the identification of 117 new proteins on our 2-D reference map of this yeast compared to the first reference map. Of these identified proteins, 40.1% were involved in metabolism. The present work provides a very useful tool for all studies relying on S. pombe as a model organism and is a considerable complement to the first reference map of S. pombe published recently by Sun and coworkers (Sun, N., Jang, J., Lee, S., Kim, S. et al.., Proteomics 2005, 5, 1574-1579).

Synthesis of fullerodendrons with an ammonium unit at the focal point and their cooperative self-assembly on a fluorescent ditopic crown ether receptor.

Dendritic branches with 1, 2, or 4 peripheral fullerene subunits and an ammonium function at the focal point have been prepared. Their ability to form self-assembled dendritic structures with oligophenylenevinylene receptors bearing one or two crown ether moieties has been evidenced by ES-MS studies for the first time. These supramolecular complexes are multicomponent photoactive devices in which the emission of the central receptor is dramatically quenched by the fullerene units. This new property resulting from the association of the different molecular subunits allowed detailed investigations of the self-assembly process by means of fluorescence titrations. The binding studies have revealed positive cooperative effects for the assembly of the fullerodendrimers with the ditopic receptor. Interestingly, the stability of the supramolecular 2:1 structures increases as the size of the dendritic unit increases. This positive dendritic effect has been explained by the larger number of possible intramolecular fullerene-fullerene interactions between the two dendritic guests when the number of fullerene subunits is increased.

Identification of the glycosylation site of the adenovirus type 5 fiber protein.

The fiber protein purified from the pool of nonincorporated viral protein after infection of cells with adenovirus type 5 exists as two forms separable by reverse-phase HPLC. As determined by mass spectrometry, this heterogeneity results from a difference in one O-linked N-acetylglucosamine (GlcNac). A western blot analysis using a monoclonal antibody directed against the GlcNac motif showed that only one of the two forms reacted with the antibody, suggesting that one form carries a single GlcNac and the other form has none. The ratio of glycosylated to nonglycosylated forms of fiber, which is about 1, is conserved in assembled viruses. After digestion of glycosylated fiber with endoproteinase GluC, isolation of the glycosylated peptide by reverse-phase HPLC, and chemical derivatization using dimethylamine, the site of glycosylation was located in the fiber shaft at serine 109 by mass spectrometry. Elimination of glycosylation by site-directed mutagenesis of fiber should help to understand the function of this postranslational modification.

Roles of thioredoxin reductase during the aerobic life of Lactococcus lactis.

Thiol-disulfide bond balance is generally maintained in bacteria by thioredoxin reductase-thioredoxin and/or glutathione-glutaredoxin systems. Some gram-positive bacteria, including Lactococcus lactis, do not produce glutathione, and the thioredoxin system is presumed to be essential. We constructed an L. lactis trxB1 mutant. The mutant was obtained under anaerobic conditions in the presence of dithiothreitol (DTT). Unexpectedly, the trxB1 mutant was viable without DTT and under aerated static conditions, thus disproving the essentiality of this system. Aerobic growth of the trxB1 mutant did not require glutathione, also ruling out the need for this redox maintenance system. Proteomic analyses showed that known oxidative stress defense proteins are induced in the trxB1 mutant. Two additional effects of trxB1 were not previously reported in other bacteria: (i) induction of proteins involved in fatty acid or menaquinone biosynthesis, indicating that membrane synthesis is part of the cellular response to a redox imbalance, and (ii) alteration of the isoforms of the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GapB). We determined that the two GapB isoforms in L. lactis differed by the oxidation state of catalytic-site cysteine C152. Unexpectedly, a decrease specific to the oxidized, inactive form was observed in the trxB1 mutant, possibly because of proteolysis of oxidized GapB. This study showed that thioredoxin reductase is not essential in L. lactis and that its inactivation triggers induction of several mechanisms acting at the membrane and metabolic levels. The existence of a novel redox function that compensates for trxB1 deficiency is suggested.

Proteomic analysis of grapevine (Vitis vinifera L.) tissues subjected to herbicide stress.

Two-dimensional gel electrophoresis coupled to mass spectrometry analysis was used to examine for the first time the effect of a herbicide (flumioxazin) on a crop species (Vitis vinifera L.) at the proteome level. Examination of 2-D maps derived from chemically stressed tissues revealed the presence of 33 spots displaying a differential expression pattern. The presence of stress responsive proteins in the different plant organs analysed suggests that flumioxazin could act systemically. Among the responsive proteins, some photosynthesis-related proteins, including several fragments of the enzyme Rubisco, were identified. This effect suggests that photosynthesis could be impaired by the herbicide. The induction of several enzymatic antioxidant systems was also observed, probably as a result of an oxidative stress. Moreover, the photorespiration pathway was stimulated, as suggested by the induction of some key enzymes involved in this process. Changes in carbon metabolism-associated proteins presumably reflect altered patterns of carbon flux in response to impaired photosynthesis and an increased need for osmotic adjustment in affected tissues. Finally, plant defences were stimulated as revealed by the induction of a set of proteins belonging to the pathogenesis-related 10 class, suggesting that they could play an essential role in cell defence mechanisms against flumioxazin.

Proteomic consequences of a human mitochondrial tRNA mutation beyond the frame of mitochondrial translation.

Numerous severe neurodegenerative and neuromuscular disorders, characterized biochemically by strong perturbations in energy metabolism, are correlated with single point mutations in mitochondrial genes coding for transfer RNAs. Initial comparative proteomics performed on wild-type and Myoclonic Epilepsy and Ragged Red Fibers (MERRF) mitochondria from sibling human cybrid cell lines revealed the potential of this approach. Here a quantitative analysis of several hundred silver-stained spots separated by two-dimensional gel electrophoresis was performed in the specific case of a couple of mitochondria, containing or not mutation A8344G in the gene for mitochondrial tRNALys, correlated with MERRF syndrome. Computer-assisted analysis allowed us to detect 38 spots with significant quantitative variations, of which 20 could be assigned by mass spectrometry. These include nuclear encoded proteins located in mitochondria such as respiratory chain subunits, metabolic enzymes, a protein of the mitochondrial translation machinery, and cytosolic contaminants. Furthermore, Western blotting combined with mass spectrometry revealed the occurrence of numerous isoforms of pyruvate dehydrogenase subunits, with subtle changes in post-translational modifications. This comparative proteomic approach gives the first insight for nuclear encoded proteins that undergo the largest quantitative changes, and pinpoints new potential molecular partners involved in the cascade of events that connect genotype to phenotype.

Self-assembly mechanism of a bimetallic europium triple-stranded helicate.

We report the self-assembly process of a supramolecular edifice based on the coordination of europium(III) by a ditopic strand L bearing tridentate bis(benzimidazolyl)pyridine subunits. Varying the metal/ligand ratio and using a fruitful combination of electrospray mass spectrometry and absorption spectrophotometry, we characterized three major complexes (EuL(2), Eu(2)L(2), and Eu(2)L(3)) in acetonitrile. Kinetic investigations showed an alternative "braiding" and "keystone" mechanism leading to Eu(2)L(3). The formation mechanism of the dinuclear triple-stranded helicate, which is mainly governed by electrostatic interactions, goes via the "side-by-side" Eu(2)L(2) intermediate. Our thermodynamic and kinetic data allow the prediction of the apparent "magic" self-assembly of Eu(2)L(3) which is fast and efficient only under a strict set of conditions.