Organelle proteomics of rat synaptic proteins: correlation-profiling by isotope-coded affinity tagging in conjunction with liquid chromatography-tandem mass spectrometry to reveal post-synaptic density specific proteins

Organelle proteomics is the method of choice for global analysis of cellular proteins. However, it is difficult to isolate organelles to homogeneity. Recently, correlation-profiling has been used to filter off the contaminants ad hoc and to disclose the genuine organelle-specific proteins. In the present study, we further extend the method to include subcellular compartments that contain proteins shared by multiple distinct subcellular domains. We performed correlation profiling of proteins contained in synaptic membrane and postsynaptic density (PSD) fractions isolated from rat brain. Proteins were labeled with isotope-coded affinity-tag reagents, digested with trypsin, and resulting peptides were resolved by cation exchange chromatography followed by reversed phase chromatography. Peptides were then subjected to mass spectrometry for quantification and identification. We confirm that the core PSD proteins were enriched in the PSD preparation. Other functional protein groups such as cytoskeleton-associated proteins, protein kinases and phosphatases, signaling components and regulators, as well as proteins involved in energy production partitioned to multiple organelles. When analyzed as groups, they were shown to accumulate to a lesser extent. Mitochondrial proteins and transporters were generally strongly depleted from the PSD fraction confirming that they were contaminants of the PSD preparation. Finally, immunoelectron microscopy was performed on selected proteins to validate the proteomics results, and confirm that synaptophysin that was highly depleted in the PSD preparation is localized in the presynaptic compartment, whereas LASP-1 that was slightly enriched in the PSD preparation is present in the PSD as well as other subdomains within the synapse.     

Mechanism of Ca2+ activation of the NADPH oxidase 5 (NOX5)

NADPH oxidase 5 (NOX5) is a homologue of the gp91(phox) subunit of the phagocyte NADPH oxidase. NOX5 is expressed in lymphoid organs and testis and distinguished from the other NADPH oxidases by its unique N terminus, which contains three canonical EF-hands, Ca(2+)-binding domains. Upon heterologous expression, NOX5 was shown to generate superoxide in response to intracellular Ca(2+) elevations. In this study, we have analyzed the mechanism of Ca(2+) activation of NOX5. In a cell-free system, Ca(2+) elevations triggered superoxide production by NOX5 (K(m) = 1.06 microm) in an NADPH- and FAD-dependent but cytosol-independent manner. That result indicated a role for the N-terminal EF-hands in NOX5 activation. Therefore, we generated recombinant proteins of NOX5 N terminus and investigated their interactions with Ca(2+). Flow dialysis experiments showed that NOX5 N terminus contained four Ca(2+)-binding sites and allowed us to define the hitherto unidentified fourth, non-canonical EF-hand. The EF-hands of NOX5 formed two pairs: the very N-terminal pair had relatively low affinity for Ca(2+), whereas the more C-terminal pair bound Ca(2+) with high affinity. Ca(2+) binding caused a marked conformation change in the N terminus, which exposed its hydrophobic core, and became able to bind melittin, a model peptide for calmodulin targets. Using a pull-down assay, we demonstrate that the regulatory N terminus and the catalytic C terminus of NOX5 interact in a Ca(2+)-dependent way. Our results indicate that the Ca(2+)-induced conformation change of NOX5 N terminus led to enzyme activation through an intra-molecular interaction. That represents a novel mechanism of activation among NAD(P)H oxidases and Ca(2+)-activated enzymes.     

MGluRs regulate the expression of neuronal calcium sensor proteins NCS-1 and VILIP-1 and the immediate early gene arg3.1/arc in the hippocampus in vivo

The metabotropic glutamate receptor (mGluR) agonist (R,S)-3,5-dihydroxyphenylglycine (DHPG) is involved in several forms of hippocampal synaptic plasticity. DHPG application can induce slow-onset potentiation, a form of long-term potentiation (LTP), in the dentate gyrus and in the CA1 region in vivo. The induction of LTP correlates with increased expression levels of neuronal calcium sensor (NCS), considered as key elements for plasticity. In this study we investigated mGluR- and time-dependent changes in the expression of two different NCS proteins. Following DHPG application in vivo NCS-1 and VILIP-1 expression increased, with significant levels reached after 8 and 24h. The effect was attenuated by treatment with the group I mGluR specific antagonist S-4-carboxyphenylglycine. The immediate early gene (IEG) arg3.1/arc showed highest expression levels 2h after DHPG-treatment. Therefore, mGluRs at concentrations which induce synaptic plasticity regulate the expression of IEGs and NCS proteins in different time frames and thus contribute to late phases of synaptic plasticity.     

Lessons from the stem cell proteome

The proteome of a cell is a molecular fingerprint directly relating to the gene expression snapshot profile at a certain point of time or developmental stage. Monitoring the expansion and the differentiation state of stem cells by proteomic means seems therefore a very attractive method for diagnostic as well as for therapeutic purposes. We have investigated the protein expression patterns of umbilical cord blood-derived CD34+/AC133+ cells in order to obtain a most comprehensive view of the stem cell proteome. For this purpose, we have applied 2-D gel electrophoresis and 2-D chromatography for most efficient protein/peptide separation and characterisation. The proteins were identified after tryptic digestion by nano-HPLC coupled directly to an ion trap mass spectrometer. An extensive bioinformatic analysis of the protein obtained revealed a dynamic stem cell proteome. This means that the heterogeneity of protein expression patterns obtained from different stem cell preparations refers to a limited set of stem cell-specific house keeping proteins as well as to a large number of proteins which depend on (marginal) stimuli from the environment. Since those are difficult to standardise, snapshot views of the stem cell proteome reflect not only stem cell-intrinsic metabolism but also the strong influence of the sample history on protein expression patterns.     

Influence of a Fusarium culmorum inoculation of wheat on the progression of mycotoxin accumulation, ingredient concentrations and ruminal in sacco dry matter degradation of wheat residues

The Fusarium head blight (FHB)-susceptible winter wheat cv. Ritmo was inoculated with spores of Fusarium culmorum at the beginning of full blossom. Samples of whole wheat plants were taken once weekly from anthesis until harvest and subsequently fractionated into straw, glumes and spindles, which were examined for deoxynivalenol (DON) and zearalenone (ZON). Additionally, the content of crude protein (CP) and non-starch polysaccharides (NSP) was scrutinized. Synthesis of the Fusarium toxins DON and ZON generally differed in terms of date of formation and concentration. Final mean DON concentrations of 37.5, 28.1 and 5.0 mg/kg DM were measured in glumes, spindles and straw, respectively, at the time of harvest. At this time, maximal mean ZON concentrations of 587, 396 and 275 microg/kg DM in spindles, glumes and straw, respectively, were determined. Moreover, Fusarium infected wheat residues contained higher CP but lower NSP contents at the last three sampling dates. In addition, collective samples of wheat straw and chaff were taken to investigate the effect of the Fusarium contamination on their in sacco DM degradation in dairy cows. Samples were analysed for mycotoxins and selected quality parameters. The dried and milled collective samples of straw and chaff were weighed into nylon bags and subjected to ruminal incubation for 4, 8, 16, 24, 48, 72, 96 and 120 h in two dairy cows equipped with a permanent rumen cannula. Marked differences in level of mycotoxin contamination as well as in ingredient composition between the variants of straw and chaff were detected. Moreover, after 120 h rumen incubation the in sacco DM degradation of inoculated straw and chaff were lower compared to the accordant controls. The soluble fraction was increased in inoculated samples, whereas a diminishment in the potentially degradable but insoluble fraction was more pronounced. Thereby, a decrease in the potential degradability was obtained for inoculated straw and even if less pronounced for chaff compared to the non inoculated corresponding controls. In conclusion, infection with F. culmorum of wheat involves an increased risk of mycotoxin contamination in straw. Also, a Fusarium infection may have an impact on chemical composition and may result in Fusarium growth-related modifications of host cell wall components.     

Identification of serotonin 5-HT1A receptor partial agonists in ginger

Animal studies suggest that ginger (Zingiber officinale Roscoe) reduces anxiety. In this study, bioactivity-guided fractionation of a ginger extract identified nine compounds that interact with the human serotonin 5-HT_1A receptor with significant to moderate binding affinities (K_i = 3–20 μΜ). [³⁵S]-GTPγS assays indicated that 10-shogaol, 1-dehydro-6-gingerdione, and particularly the whole lipophilic ginger extract (K_i = 11.6 μg/ml) partially activate the 5-HT_1A receptor (20–60% of maximal activation). In addition, the intestinal absorption of gingerols and shogaols was simulated and their interactions with P-glycoprotein were measured, suggesting a favourable pharmacokinetic profile for the 5-HT_1A active compounds.     

Containment of Extended Length Polymorphisms in Silk Proteins

The spider silk gene family to the current date has been developed by gene duplication and homogenization events as well as conservation of crucial sequence parts. These evolutionary processes have created an amazing diversity of silk types each associated with specific properties and functions. In addition, they have led to allelic and gene variants within a species as exemplified by the major ampullate spidroin 1 gene of Nephila clavipes. Due to limited numbers of individuals screened to date little is known about the extent of these heterogeneities and how they are finally manifested in the proteins. Using expanded sample sizes, we show that sequence variations expressed as deletions or insertions of tri-nucleotides lead to different sized and structured repetitive units throughout a silk protein. Moreover, major ampullate spidroins 1 can quite dramatically differ in their overall lengths; however, extreme variants do not spread widely in a spider population. This suggests that a certain size range stabilized by purifying selection is important for spidroin 1 gene integrity and protein function. More than one locus for spidroin 1 genes possibly exist within one individual genome, which are homogenized in size, are differentially expressed and give a spider a certain degree of adaptation on silk’s composition and properties. Such mechanisms are shared to a lesser extent by the second major ampullate spidroin gene.     

Calnexin Deficiency Leads to Dysmyelination

Calnexin is a molecular chaperone and a component of the quality control of the secretory pathway. We have generated calnexin gene-deficient mice (cnx^−/−) and showed that calnexin deficiency leads to myelinopathy. Calnexin-deficient mice were viable with no discernible effects on other systems, including immune function, and instead they demonstrated dysmyelination as documented by reduced conductive velocity of nerve fibers and electron microscopy analysis of sciatic nerve and spinal cord. Myelin of the peripheral and central nervous systems of cnx^−/− mice was disorganized and decompacted. There were no abnormalities in neuronal growth, no loss of neuronal fibers, and no change in fictive locomotor pattern in the absence of calnexin. This work reveals a previously unrecognized and important function of calnexin in myelination and provides new insights into the mechanisms responsible for myelin diseases.     

WindowMasker: window-based masker for sequenced genomes

MOTIVATION: Matches to repetitive sequences are usually undesirable in the output of DNA database searches. Repetitive sequences need not be matched to a query, if they can be masked in the database. RepeatMasker/Maskeraid (RM), currently the most widely used software for DNA sequence masking, is slow and requires a library of repetitive template sequences, such as a manually curated RepBase library, that may not exist for newly sequenced genomes. RESULTS: We have developed a software tool called WindowMasker (WM) that identifies and masks highly repetitive DNA sequences in a genome, using only the sequence of the genome itself. WM is orders of magnitude faster than RM because WM uses a few linear-time scans of the genome sequence, rather than local alignment methods that compare each library sequence with each piece of the genome. We validate WM by comparing BLAST outputs from large sets of queries applied to two versions of the same genome, one masked by WM, and the other masked by RM. Even for genomes such as the human genome, where a good RepBase library is available, searching the database as masked with WM yields more matches that are apparently non-repetitive and fewer matches to repetitive sequences. We show that these results hold for transcribed regions as well. WM also performs well on genomes for which much of the sequence was in draft form at the time of the analysis. AVAILABILITY: WM is included in the NCBI C++ toolkit. The source code for the entire toolkit is available at ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/. Once the toolkit source is unpacked, the instructions for building WindowMasker application in the UNIX environment can be found in file src/app/winmasker/README.build. SUPPLEMENTARY INFORMATION: Supplementary data are available at ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/windowmasker/windowmasker_suppl.pdf