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Oxidation and reduction of protein cysteinyl thiols serve as molecular switches, which is considered the most central mechanism for redox regulation of biological processes, altering protein structure, biochemical activity, subcellular localization, and binding affinity. Redox proteomics allows for the global identification of redox-modified cysteine (Cys) sites and quantification of their oxidation/reduction responses, serving as a hypothesis-generating platform to stimulate redox biology mechanistic research. Here, we developed Simultaneous Protein Expression and Redox (SPEAR) analysis, a new redox-proteomics approach based on differential labeling of oxidized and reduced cysteines with light and heavy isotopic forms of commercially available isotopically-labeled N-ethylmaleimide (NEM). The presented method does not require enrichment for labeled peptides, thus enabling simultaneous quantification of Cys oxidation state and protein abundance. Using SPEAR, we were able to quantify the in-vivo oxidation state of thousands of cysteines across the Arabidopsis proteome under steady-state and oxidative stress conditions. Functional assignment of the identified redox-sensitive proteins demonstrated the widespread effect of oxidative conditions on various cellular functions and highlighted the enrichment of chloroplast-targeted proteins. SPEAR provides a simple, straightforward, and cost-effective means of studying redox proteome dynamics. The presented data provide a global quantitative view of cysteine oxidation of well-known redox-regulated active sites and many novel redox-sensitive sites whose role in plant acclimation to stress conditions remains to be further explored.

The analysis of cells and tissue by bottom-up proteomics starts with lysis, followed by in-solution digestion. Lysis buffers commonly used include detergents and other reagents for achieving efficient protein solubility. However, these reagents are, for the most part, incompatible with downstream analytical instrumentation. One method for in-solution digestion and cleanup, termed suspension trapping (S-Trap), has been recently introduced. We present an evaluation of the compatibility of commonly used lysis buffers with S-Trap: SDS, urea, NP-40, RIPA, and SDS with DTT (SDT). We show that S-Trap is compatible with all of the tested buffers, with SDS and SDT performing the best. On the basis of these data, we anticipate that the method will transform experimental planning for mass-spectrometry-based proteomics, making it far more flexible and tolerable of various lysis buffers. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD011665.

The highly conserved COP9 signalosome (CSN) complex is a key regulator of all cullin-RING-ubiquitin ligases (CRLs), the largest family of E3 ubiquitin ligases. Until now it was accepted that the CSN is comprised of eight canonical components. Here, we report the discovery of an additional integral and stoichiometric subunit that thus far evaded detection, and named it CSNAP (CSN Acidic Protein). We show that CSNAP binds CSN3, CSN5 and CSN6 and its incorporation into the CSN complex is mediated through the C-terminal region involving conserved aromatic residues. Moreover, depletion of this small protein influences the cell phenotype, leading to reduced proliferation, and a flattened and enlarged morphology. Finally, based on sequence and structural properties shared by both CSNAP and DSS1, a component of the related 19S lid proteasome complex, we propose that CSNAP, the ninth CSN subunit, is the missing paralogous subunit of DSS1.

Presented is a data set for benchmarking MS1-based label-free quantitative proteomics using a quadrupole orbitrap mass spectrometer. Escherichia coli digest was spiked into a HeLa digest in four different concentrations, simulating protein expression differences in a background of an unchanged complex proteome. The data set provides a unique opportunity to evaluate the proteomic platform (instrumentation and software) in its ability to perform MS1-intensity-based label-free quantification. We show that the presented combination of informatics and instrumentation produces high precision and quantification accuracy. The data were also used to compare different quantitative protein inference methods such as iBAQ and Hi-N. The data can also be used as a resource for development and optimization of proteomics informatics tools, thus the raw data have been deposited to ProteomeXchange with identifier PXD001385.

Stimulation of Escherichia coli with acetate elevates the acetylation level of the chemotaxis response regulator CheY. This elevation, in an unknown mechanism, activates CheY to generate clockwise rotation. Here, using quantitative selective reaction monitoring mass spectrometry and high-resolution targeted mass spectrometry, we identified K91 and K109 as the major sites whose acetylation level in vivo increases in response to acetate. Employing single and multiple lysine replacements in CheY, we found that K91 and K109 are also the sites mainly responsible for acetate-dependent clockwise generation. Furthermore, we showed that clockwise rotation is repressed when residue K91 is nonmodified, as evidenced by an increased ability of CheY to generate clockwise rotation when K91 was acetylated or replaced by specific amino acids. Using molecular dynamics simulations, we show that K91 repression is manifested in the conformational dynamics of the β4α4 loop, shifted toward an active state upon mutation. Removal of β4α4 loop repression may represent a general activation mechanism in CheY, pertaining also to the canonical phosphorylation activation pathway as suggested by crystal structures of active and inactive CheY from Thermotoga maritima. By way of elimination, we further suggest that K109 acetylation is actively involved in generating clockwise rotation.

Traditional "bottom-up" proteomic approaches use proteolytic digestion, LC-MS/MS, and database searching to elucidate peptide identities and their parent proteins. Protein sequences absent from the database cannot be identified, and even if present in the database, complete sequence coverage is rarely achieved even for the most abundant proteins in the sample. Thus, sequencing of unknown proteins such as antibodies or constituents of metaproteomes remains a challenging problem. To date, there is no available method for full-length protein sequencing, independent of a reference database, in high throughput. Here, we present Database-independent Protein Sequencing, a method for unambiguous, rapid, database-independent, full-length protein sequencing. The method is a novel combination of non-enzymatic, semi-random cleavage of the protein, LC-MS/MS analysis, peptide de novo sequencing, extraction of peptide tags, and their assembly into a consensus sequence using an algorithm named "Peptide Tag Assembler." As proof-of-concept, the method was applied to samples of three known proteins representing three size classes and to a previously un-sequenced, clinically relevant monoclonal antibody. Excluding leucine/isoleucine and glutamic acid/deamidated glutamine ambiguities, end-to-end full-length de novo sequencing was achieved with 99-100% accuracy for all benchmarking proteins and the antibody light chain. Accuracy of the sequenced antibody heavy chain, including the entire variable region, was also 100%, but there was a 23-residue gap in the constant region sequence.

Diatoms are ubiquitous marine photosynthetic eukaryotes responsible for approximately 20% of global photosynthesis. Little is known about the redox-based mechanisms that mediate diatom sensing and acclimation to environmental stress. Here we used a quantitative mass spectrometry-based approach to elucidate the redox-sensitive signaling network (redoxome) mediating the response of diatoms to oxidative stress. We quantified the degree of oxidation of 3,845 cysteines in the Phaeodactylum tricornutum proteome and identified approximately 300 redox-sensitive proteins. Intriguingly, we found redox-sensitive thiols in numerous enzymes composing the nitrogen assimilation pathway and the recently discovered diatom urea cycle. In agreement with this finding, the flux from nitrate into glutamine and glutamate, measured by the incorporation of (15)N, was strongly inhibited under oxidative stress conditions. Furthermore, by targeting the redox-sensitive GFP sensor to various subcellular localizations, we mapped organelle-specific oxidation patterns in response to variations in nitrogen quota and quality. We propose that redox regulation of nitrogen metabolism allows rapid metabolic plasticity to ensure cellular homeostasis, and thus is essential for the ecological success of diatoms in the marine ecosystem.

In this paper we describe the synthesis of chiral mesoporous silica based on chiral block copolymers of poly(ethylene oxide) and of d-phenylalanine (PEO-b-D-Phe) as a surfactant template. The resulting porous structures are characterized by nitrogen sorption experiments, transmission electron microscopy, and small-angle XRD. It is shown that chiral block copolymers of PEO-b-D-Phe are effective as a surfactant template for the preparation of silica materials with highly ordered periodic mesoporous structures of hexagonal symmetry with a pore size of ca. 5 nm and high surface areas of ca. 700 m2/g. The enantioselectivity feature of this porous silica, after the extraction of the chiral copolymers, was examined by selective adsorption of enantiomers and racemic solutions of valine. The selective adsorption was measured by circular dichroism (CD) spectroscopy. A chiral selectivity factor of 2.34 was found with the D enantiomer of valine adsorbed preferably.

Nanocomposites of Ag nanoparticles/mesoporous γ-Al2O3 were synthesized by sonochemical treatment of the precursors. The sonicated product consisted of Ag nanoparticles dispersed in the bayerite [Al(OH)3]/boehmite [AlO(OH)] matrix. Upon calcination under argon, the Ag nanoparticles were found to be incorporated in a mesoporous structure of γ-Al2O3. For a solid containing 3.7 wt % Ag nanoparticles, the nanoparticles remained on the surface of mesoporous alumina and hence BET surface area increased as compared to pristine γ-Al2O3, whereas for 10.5 wt % Ag nanoparticles, the surface area decreased. HRTEM studies corroborated this fact and showed that, at higher Ag concentrations, Ag nanoparticles blocked the pores and also increased the diameter of the pores of mesoporous alumina. The products with the 3.7 wt % silver concentration had uniform pores with narrow pore size distribution of the pores, although the TEM pictures indicated wormhole channel motifs. The formation of the mesoporous structure was govern...

TiO2@C core−shell composite nanoparticles were synthesized by a simple and efficient single-step method in a specially made Swagelok cell at different temperatures. The prepared samples were characterized by XRD, diffuse reflectance-UV−vis, Raman, TEM, HRTEM, and N2 adsorption−desorption methods. The carbon content in the samples can be varied with reaction time and temperature. It is evident from TEM analysis that the as-prepared samples are core−shell structures of TiO2, anatase phase, and C. The diameter of the TiO2@C nanoparticles is in the range of 15−35 nm. HRTEM results showed that a few graphitic layers were wrapped on the surface of TiO2, and these carbon layers are responsible for suppressing other phase formations of TiO2 even at high temperature. However, a few percentage points of the rutile phase are observed at high temperature (900 °C), evidenced from Raman analysis. The prepared samples were tested for their photochemical activities for 4-chlorophenol degradation. The sample prepared at 7...

In this article, a simple microwave route was applied for the synthesis of nanoflakes and dendrite-type β-indium sulfide (In2S3) in high yield (>97%), using a homogeneous mixture of indium(III)chloride and thiourea in an ethylene glycol (EG)/polyethylene glycol (PEG400) solvent. The reaction was conducted in a simple domestic microwave oven (DMO). Powder X-ray diffraction (XRD), low resolution and high resolution transmission electron microscopy (LRTEM and HRTEM), selected area electron diffraction (SAED), and energy dispersive X-ray spectroscopy (EDS), were applied to investigate the crystallinity, structure, morphology, and composition of the In2S3 nano-materials. Both the as-synthesized and calcined In2S3 products were a body-centered tetragonal (bct) phase, observed by XRD and HRTEM. The length and width of the resulting nanoflakes were in the range of 70–600 nm and 4–10 nm, respectively. The optical band gap of the powder was determined by diffuse reflectance spectroscopy (DRS) and was found to be 2.44 eV. The electronic properties of the products were studied by measuring the optical absorption spectra using photo-acoustic spectroscopy. The band gap calculated by this method was found to be 2.52 eV. A possible mechanism for the formation of nanoflakes/dendrites-type In2S3 was also discussed.

Chimeric RNAs comprise exons from two or more different genes and have the potential to encode novel proteins that alter cellular phenotypes. To date, numerous putative chimeric transcripts have been identified among the ESTs isolated from several organisms and using high throughput RNA sequencing. The few corresponding protein products that have been characterized mostly result from chromosomal translocations and are associated with cancer. Here, we systematically establish that some of the putative chimeric transcripts are genuinely expressed in human cells. Using high throughput RNA sequencing, mass spectrometry experimental data, and functional annotation, we studied 7424 putative human chimeric RNAs. We confirmed the expression of 175 chimeric RNAs in 16 human tissues, with an abundance varying from 0.06 to 17 RPKM (Reads Per Kilobase per Million mapped reads). We show that these chimeric RNAs are significantly more tissue-specific than non-chimeric transcripts. Moreover, we present evidence that chimeras tend to incorporate highly expressed genes. Despite the low expression level of most chimeric RNAs, we show that 12 novel chimeras are translated into proteins detectable in multiple shotgun mass spectrometry experiments. Furthermore, we confirm the expression of three novel chimeric proteins using targeted mass spectrometry. Finally, based on our functional annotation of exon organization and preserved domains, we discuss the potential features of chimeric proteins with illustrative examples and suggest that chimeras significantly exploit signal peptides and transmembrane domains, which can alter the cellular localization of cognate proteins. Taken together, these findings establish that some chimeric RNAs are translated into potentially functional proteins in humans. The work of M.F-M. is supported by the CNIO (Caja Navarra International Postdoctoral Program) and the Miguel Servet (FIS) grant. The work of V.L. is supported by the French ANR MIRI BLAN08-1335497 Project and the ERC Advanced Grant Sisyphe. This study is supported by the Spanish National Bioinformatics Institute (INB-ISCIII) and by grants from the Spanish Government (CONSOLIDER CSD2007-00050, BIO2007-666855, and BIO2011-26205), European Commission FP7 project ASSET (HEALTH-F4-2010-259348), and the NHGRI-NIH ENCODE grants (U54 HG00455-04 and U54 HG004557)

The synthesis of lamellar mesoporous molybdenum oxide is reported, the structure of which is retained after the removal of the surfactant template.