Metaproteomics is one of a suite of new approaches providing insights into the activities of microorganisms in natural environments. Proteins, the final products of gene expression, indicate cellular priorities, taking into account both transcriptional and posttranscriptional control mechanisms that control adaptive responses. Here, we report the proteomic composition of the < 1.2 μm fraction of a microbial community from Oregon coast summer surface waters, detected with two-dimensional liquid chromatography coupled with electrospray tandem mass spectrometry. Spectra corresponding to proteins involved in protein folding and biosynthesis, transport, and viral capsid structure were the most frequently detected. A total of 36% of all the detected proteins were best matches to the SAR11 clade, and other abundant coastal microbial clades were also well represented, including the Roseobacter clade (17%), oligotrophic marine gammaproteobacteria group (6%), OM43 clade (1%). Viral origins were attributed to 2.5% of proteins. In contrast to oligotrophic waters, phosphate transporters were not highly detected in this nutrient-rich system. However, transporters for amino acids, taurine, polyamines and glutamine synthetase were among the most highly detected proteins, supporting predictions that carbon and nitrogen are more limiting than phosphate in this environment. Intriguingly, one of the highly detected proteins was methanol dehydrogenase originating from the OM43 clade, providing further support for recent reports that the metabolism of one-carbon compounds by these streamlined methylotrophs might be an important feature of coastal ocean biogeochemistry.
metaproteomics; marine plankton; OM43 clade
The objective of this study was to develop a mass spectrometric protocol to search for proteins related to phototrophy in marine bacteria. The genes that produce proteins involved in conversion of light into energy have been detected by cloning-sequencing from some of these bacteria, but it was previously unknown if these proteins were actually expressed.
Attaining this study’s goal was complicated by the fact that the samples consisted of miniscule cell pellets, which yielded small amounts of very complex mixtures of proteins. Sample preparation and analysis were tailored to optimize the probability of detecting the proteins of interest. It has been reported that using both matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) to analyze a mixture of peptides leads to the identification of more peptides that either technique alone. In order to exploit this complementarity between ESI and MALDI for proteomic analysis, samples were analyzed using both ionization techniques. With correct choices in sample preparation and ionization process, biologically relevant proteins can be identified out of small samples containing whole proteomes.
Bacteria; MALDI; ESI; complementary; proteome
A radio frequency-free (RFF), analyzer-independent cell has been devised for electron-capture dissociation (ECD) of ions. The device is based on interleaving a series of electrostatic lenses with the periodic structure of magnetostatic lenses commonly found in a traveling wave tube. The RFF electrostatic/magnetostatic ECD cell was installed in a Finnigan TSQ700 ESI triple quadrupole (QqQ) spectrometer, and its performance was evaluated by recording product-ion spectra of doubly protonated substance P, doubly protonated gramicidin S, doubly protonated neurotensin, and triply protonated neurotensin. These spectra were readily obtained without recourse to a buffering gas or synchronizing electron injection with a specific phase of an RF field. The mass spectra produced with the modified instrument appear in all respects (other than resolution and mass accuracy, which were limited by the mass spectrometer used) to be at least as good for purposes of peptide identification as those recorded with Fourier transform ion cyclotron resonance (FT ICR) instruments; however, the effort and time to produce the mass spectra were much less than required to produce their FT ICR counterparts. The cell’s design and compact construction should allow it to be incorporated at relatively little cost into virtually any type of tandem mass spectrometer, for example, triple quadrupole, hybrid quadrupole ion trap, hybrid quadrupole time-of-flight, or even FT-ICR.
A model was used to predict the photodebromination of the BDE-203, 197, 196, and 153, the major components of the octa-polybrominated diphenyl ether (PBDE) technical mixture, as well as BDE-47, and the predicted results were compared to the experimental results. The predicted reaction time profiles of the photodebromination products correlate well with the experimental results. In addition, the slope of the linear regression between the measured product concentrations of the first step of the photodebromination products and their enthalpies of formation was found to be close to their theoretical value. The photodebromination results of the octa-BDE technical mixture were compared with anaerobic microbial debromination results and were found to be the same in both experiments. The debromination pathways of technical octa-BDE mixture were identified and BDE-154, 99, 47, and 31 were found to be the most abundant hexa-, penta-, tetra-, and tri-BDE debromination products, respectively. In addition to photodebromination and anaerobic biodebromination, the model prediction was also compared to the zero-valent iron reduction of BDE-209, 100, and 47 and the same debromination products were observed. Good correlation was observed between the photodebromination rate constants of fifteen PBDE congeners and their calculated lowest unoccupied molecular orbital (LUMO) energies, indicating that PBDE photodebromination is caused by electron transfer. Furthermore, the rate constants for the three different PBDE debromination processes are controlled by C–Br bond dissociation energy. With the model from the present study, the major debromination products for any PBDE congener released into the environment can be predicted.
Polybrominated diphenyl ether; Model; Photodegradation; Anaerobic microbial debromination
The use of isobaric tagging for relative and absolute quantification (iTRAQ) has increased dramatically over the past few years. Many factors can affect the accuracy of quantification. Some of these include the number of biological/technical replicates, sample complexity, instrumentation, method of peptide/protein identification and the statistical techniques used for data analysis. It has been observed that the low collision energies normally used in electrospray ionization quadrupole time-of-flight (ESI QTOF) can result in low iTRAQ reporter ion abundances. We used two-way analysis of variance (ANOVA) to compare the iTRAQ ratios that were generated on an ESI QTOF and a matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI TOF/TOF). It appears that iTRAQ analyses performed on an ESI QTOF without any special modifications to instrumental parameters produce essentially the same protein ratios as those obtained on a MALDI TOF/TOF.
Fluorochemicals are persistent contaminants that are globally distributed in air, water, sediments, and biota. Wastewater treatment plants (WWTPs) play an important role in mitigating pollutant releases from municipalities to aquatic and terrestrial environments. However, because WWTPs are point sources of fluorochemicals, it is important to understand their contribution to fluorochemical burdens in the greater context of watersheds. To this end, over a 1 week period, the mass flows of 11 fluorochemicals from seven WWTPs that discharge effluent into the Glatt River in Switzerland were measured and compared to the measured mass flows within the Glatt River. Overall, the fluorochemicals were not removed efficiently during wastewater treatment. Effluents from WWTPs and Glatt River water were dominated by perfluorooctane sulfonate, which was detected in all samples, followed by perfluorohexane sulfonate and perfluorooctanoate. The mass flows of fluorochemicals emanating from WWTPs were found to be conserved within the 35 km Glatt River, which indicates that input from the WWTPs is additive and that removal within the Glatt River is not significant. Per capita discharges of fluorochemicals were calculated from the populations served by the WWTPs studied; the values determined also account for the fluorochemical content of Lake Greifen (Greifensee), which is a lake at the headwaters of the Glatt River that also receives treated wastewater.
With the phaseout of the manufacture of some polybrominated diphenyl ether (PBDE) formulations, namely penta-brominated diphenyl ether (BDE) and octa-BDE, and the continued use of the deca-BDE formulation, it is important to be able to predict the photodegradation of the more highly brominated congeners. A model was developed and validated to predict the products and their relative concentrations from the photodegradation of PBDEs. The enthalpies of formation of the 209 PBDE congeners were calculated, and the relative reaction rate constants were obtained. The predicted reaction rate constants for PBDEs show linear correlation with previous experimental results. Because of their large volume use, their presence in the environment, and/or importance in the photodegradation of the deca-BDE formulation, BDE-209, BDE-184, BDE-100, and BDE-99 were chosen for further ultraviolet photodegradation experiments in isooctane. The photodegradation model successfully predicted the products of the photochemical reactions of PBDEs in experimental studies. A gas chromatography retention time model for PBDEs was developed using a multiple linear regression analysis and, together with the photodegradation model and additional PBDE standards, provided a way to identify unknown products from PBDE photodegradation experiments. Based on the results of the photodegradation experiments, as well as the model predictions, it appears that the photodegradation of PBDEs is a first-order reaction and, further, that the rate-determining step is the stepwise loss of bromine. Our results suggest that, based on photodegradation, over time, BDE-99 will remain the most abundant penta-BDE, while BDE-49 and BDE-66 will increase greatly and will be comparable in abundance to BDE-47.
Polybrominated diphenyl ether; Photodegradation; Model; Theoretical calculation
Resonant electron capture by Gly, Ala and Phe esters have shown that the most efficient negative ion (NI) fragmentations are associated with the C-termini. A new mechanism for the negative ion-forming processes at energies lower than those associated with the π*OO shape resonance involves coupling between dipole-bound and valence negative ion states of the same symmetry for amino acid conformers with high permanent dipoles. The interaction avoids crossing of the NI states and instead leads to formation of two adiabatic potential energy surfaces. Underivatized amino acids most effectively fragment from the bottom adiabatic surface via generation of [M-H]− carboxylate anions by hydrogen-atom tunneling through the barrier; fragmentation of the their esters with formation of analogues [M-X]− NIs occurs through the upper adiabatic state without penetration of the barrier in which the energy of the valence σ*OX resonance exceeds the bond dissociation energy of the neutral molecule. Low and high temperature resonant electron capture experiments point to the importance of conformational preferences of the amino acids for optimum dissociation of the parent NIs in the gas phase.
Resonant electron capture mass spectrometry; negative ions; amino acids; esterification
We used a proteomic approach to identify novel proteins that may regulate metabotropic glutamate receptor 5 (mGluR5) responses by direct or indirect protein interactions. This approach does not rely on the heterologous expression of proteins and offers the advantage of identifying protein interactions in a native environment. The mGluR5 protein was immunoprecipitated from rat brain lysates; co-immunoprecipitating proteins were analyzed by mass spectrometry and identified peptides were matched to protein databases to determine the correlating parent proteins. This proteomic approach revealed the interaction of mGluR5 with known regulatory proteins, as well as novel proteins that reflect previously unidentified molecular constituents of the mGluR5-signaling complex. Immunoblot analysis confirmed the interaction of high confidence proteins, such as phosphofurin acidic cluster sorting protein 1, microtubule-associated protein 2a and dynamin 1, as mGluR5-interacting proteins. These studies show that a proteomic approach can be used to identify candidate interacting proteins. This approach may be particularly useful for neurobiology applications where distinct protein interactions within a signaling complex can dramatically alter the outcome of the response to neurotransmitter release, or the disruption of normal protein interactions can lead to severe neurological and psychiatric disorders.
mass spectrometry; metabotropic glutamate receptor; protein interaction; proteomics
“Candidatus Pelagibacter ubique,” an abundant marine alphaproteobacterium, subsists in nature at low ambient nutrient concentrations and may often be exposed to nutrient limitation, but its genome reveals no evidence of global regulatory mechanisms for adaptation to stationary phase. High-resolution capillary liquid chromatography coupled online to an LTQ mass spectrometer was used to build an accurate mass and time (AMT) tag library that enabled quantitative examination of proteomic differences between exponential- and stationary-phase “Ca. Pelagibacter ubique” cells cultivated in a seawater medium. The AMT tag library represented 65% of the predicted protein-encoding genes. “Ca. Pelagibacter ubique” appears to respond adaptively to stationary phase by increasing the abundance of a suite of proteins that contribute to homeostasis rather than undergoing a major remodeling of its proteome. Stationary-phase abundances increased significantly for OsmC and thioredoxin reductase, which may mitigate oxidative damage in “Ca. Pelagibacter,” as well as for molecular chaperones, enzymes involved in methionine and cysteine biosynthesis, proteins involved in ρ-dependent transcription termination, and the signal transduction enzyme CheY-FisH. We speculate that this limited response may enable “Ca. Pelagibacter ubique” to cope with ambient conditions that deprive it of nutrients for short periods and, furthermore, that the ability to resume growth overrides the need for a more comprehensive global stationary-phase response to create a capacity for long-term survival.
A quantitative method was developed for the determination of fluorinated alkyl substances in municipal wastewater influents and effluents. The method consisted of centrifugation followed by large-volume injection (500 μL) of the supernatant onto a liquid chromatograph with a reverse-phase column and detection by electrospray ionization, and tandem mass spectrometry (LC/MS/MS). The fluorinated analytes studied include perfluoroalkyl sulfonates, fluorotelomer sulfonates, perfluorocarboxylates, and select fluorinated alkyl sulfonamides. Recoveries of the fluorinated analytes from wastewater treatment plant (WWTP) raw influents and final effluent ranged from 77% – 96% and 80% – 99%, respectively. The lower limit of quantitation ranged from 0.5 to 3.0 ng/L depending on the analyte. The method was applied to flow-proportional composites of raw influent and final effluent collected over a 24 hr period from ten WWTPs nationwide. Fluorinated alkyl substances were observed in wastewater at all treatment plants and each plant exhibited unique distributions of fluorinated alkyl substances despite similarities in treatment processes. In nine out of the ten plants sampled, at least one class of fluorinated alkyl substances exhibited increased concentrations in the effluent as compared to the influent concentrations. In some instances, decreases in certain fluorinated analyte concentrations were observed and attributed to sorption to sludge.
Fluorochemicals have widespread applications and are released into municipal wastewater treatment plants via domestic wastewater. A field study was conducted at a full-scale municipal wastewater treatment plant to determine the mass flows of selected fluorochemicals. Flow-proportional, 24-h samples of raw influent, primary effluent, trickling filter effluent, secondary effluent, and final effluent and grab samples of primary, thickened, activated, and anaerobically-digested sludge were collected over ten days and analyzed by liquid chromatography electrospray-ionization tandem mass spectrometry. Significant decreases in the mass flows of perfluorohexane sulfonate and perfluorodecanoate occurred during trickling filtration and primary clarification, while activated sludge treatment decreased the mass flow of perfluorohexanoate. Mass flows of the 6:2 fluorotelomer sulfonate and perfluorooctanoate were unchanged as a result of wastewater treatment, which indicates that conventional wastewater treatment is not effective for removal of these compounds. A net increase in the mass flows for perfluorooctane and perfluorodecane sulfonates occurred from trickling filtration and activated sludge treatment. Mass flows for perfluoroalkylsulfonamides and perfluorononanoate also increased during activated sludge treatment and are attributed to degradation of precursor molecules.
In this report, the effectiveness of high performance liquid chromatography (HPLC) in conjunction with electrospray ionization mass spectrometry (ESI-MS) is examined as a tool for identifying the sites of crosslinking in a protein that has been photoreacted with a non-photolabeled oligonucleotide. ESI-MS and MALDI-MS analyses preceded by off-line microflow and nanoflow HPLC, on-line microflow HPLC/ESI, and on-line nanoflow HPLC/ESI interfaces were performed in order to determine their relative effectiveness in separating mixtures of nucleopeptides and identifying sites of crosslinking on the individual components. The characteristics of these four techniques as well as possibilities for improving the analysis of nucleopeptides by ESI MS are compared and discussed.
The filamentous virion of the closterovirus Beet yellows virus (BYV) consists of a long body formed by the major capsid protein (CP) and a short tail composed of the minor capsid protein (CPm) and the virus-encoded Hsp70 homolog. By using nano-liquid chromatography-tandem mass spectrometry and biochemical analyses, we show here that the BYV 64-kDa protein (p64) is the fourth integral component of BYV virions. The N-terminal domain of p64 is exposed at the virion surface and is accessible to antibodies and mild trypsin digestion. In contrast, the C-terminal domain is embedded in the virion and is inaccessible to antibodies or trypsin. The C-terminal domain of p64 is shown to be homologous to CP and CPm. Mutation of the signature motifs of capsid proteins of filamentous RNA viruses in p64 results in the formation of tailless virions, which are unable to move from cell to cell. These results reveal the dual function of p64 in tail assembly and BYV motility and support the concept of the virion tail as a specialized device for BYV cell-to-cell movement.