Analysis of E. coli soluble proteins by non‐denaturing micro 2‐DE/3‐DE and MALDI‐MS‐PMF

Escherichia coli (strain K‐12)‐soluble proteins were analyzed by nondenaturing micro 2‐DE and MALDI‐MS‐PMF. The reported conditions of nondenaturing IEF in agarose column gels [Jin, Y., Manabe, T., Electrophoresis 2009, 30, 939–948] were modified to optimize the resolution of cellular soluble proteins. About 300 CBB‐stained spots, the apparent molecular masses of which ranged from ca. 6000 to 10 kDa, were detected. All the spots on two reference 2‐DE gels (one for wide mass range and one for low‐molecular‐mass range) were numbered and subjected to MALDI‐MS‐PMF for the assignment of constituting polypeptides. Most of the spots (310 spots out of 329) provided significant match (p<0.05) with polypeptides in Swiss‐Prot database and totally 228 polypeptide species were assigned. Activity staining of enzymes such as alkaline phosphatase and catalases was performed on the 2‐DE gels and the locations of the activity spots matched well with those of the MS‐assigned polypeptides of the enzymes. Most of the polypeptides with subunit information in Swiss‐Prot (119 polypeptides as homo‐multimers and 25 as hetero‐multimers out of the 228), such as pyruvate dehydrogenase complex which is composed of three enzymatic components, were detected at the apparent mass positions of their polymers, suggesting that the proteins were separated retaining their subunit structures. When a nondenaturing 2‐DE gel was vertically cut into 2 mm strips and one of the strips was subjected to a third‐dimension micro SDS‐PAGE (micro 3‐DE), about 190 CBB‐stained spots were detected. The assignment of the polypeptides separated on the 3‐DE gel would further provide information on protein/polypeptide interactions.     

Determination of RH‐5849 and indoxacarb in rice straw,rice husk,brown rice and soil using liquid chromatography–tandem triple quadrupole mass spectrometry following extraction with QuEChERS method

A fast and simple analytical method was developed for the simultaneous determination of RH‐5849 and indoxacarb in soil, rice straw, rice husk and brown rice. QuEChERS (quick, easy, cheap, effective, rugged and safe) method was used for extraction, and liquid chromatography with tandem triple quadrupole mass spectrometry was used for quantification. The matrix‐matched calibration plots were linear in the range between 25 and 5000 μg/L for soil, rice straw, rice husk and brown rice samples. All determination coefficients (R²) were ≥0.9962. The limits of detection and quantification were 1.5 and 5 μg/kg, respectively. Recoveries at three fortification levels ranged between 79.5 and 97.9% with relative standard deviations <11%. The developed method was validated and applied for the analysis of dissipation study samples. For field experiments, the half‐lives of RH‐5849 and indoxacarb in rice straw were 11.93 and 5.83 days, respectively. The method was demonstrated to be reliable for the routine monitoring of RH‐5849 and indoxacarb in rice samples. Copyright © 2016 John Wiley & Sons, Ltd.     

Performance of nondenaturing micro 2-DE followed by third-dimension SDS-PAGE in the analysis of Escherichia coli soluble proteins

In a previous paper, we reported on the analysis of Escherichia coli (strain K‐12) soluble proteins by nondenaturing micro 2‐DE/3‐DE and MALDI‐MS‐PMF [Manabe, T., Jin, Y., Electrophoresis 2010, 31, 2740–2748]. To evaluate the performance of the 2‐DE/3‐DE technique, a nondenaturing 2‐DE gel just after the second‐dimension run was cut into 12 vertical strips, each 2 mm‐wide strip was set on a micro slab gel, and third‐dimension SDS‐PAGE was run in parallel. Each of the twelve 3‐DE gels showed about 150–200 CBB‐stained spots. Two of the 3‐DE gels were selected for the assignment of polypeptides using MALDI‐MS‐PMF and totally 161 polypeptides were assigned on the two 3‐DE gels, in which 81 have been assigned on the nondenaturing micro 2‐DE gel and 80 were newly assigned. Most of the newly assigned polypeptides resided in faintly stained spots on the 3‐DE gels, which indicates that the polypeptides were purified in the process of the third‐dimension separation. The comparisons of the apparent mass values estimated from the second‐dimension (nondenaturing pore‐gradient PAGE) mobility with those estimated from the third‐dimension (SDS‐PAGE) mobility suggested the oligomer structures of the assigned polypeptides and they matched well with those described in a database (UniProtKnowledgebase). The technique of nondenaturing micro 2‐DE/3‐DE, combined with MALDI‐MS‐PMF, could become an efficient method to obtain information on the quaternary structures of hundreds of cellular soluble proteins simultaneously because of its high efficiency in protein/polypeptide separation and assignment.     

Electrophoretic and zymographic characterization of proteins isolated by various extraction methods from ejaculated and capacitated boar sperms

The presented work focuses on electrophoretic and zymographic characterization of boar sperm proteins isolated by various extraction methods and on comparison of the protein profiles obtained from ejaculated and in vitro capacitated spermatozoa. Sperm proteins of ejaculated and in vitro capacitated boar sperms were isolated with the following agents: 1% v/v Triton X‐100, 1% v/v Triton X‐114, 2% v/v acetic acid, 1% m/v sodium dodecyl sulphate (SDS), 30 mM N‐octyl‐β‐D ‐glucopyranoside (OBG), rehydration buffer (RHB) for isoelectric focusing and finally by the freezing–thawing approach. The extracts were characterized in terms of 1‐DE, 2‐DE protein profiles, 1‐DE glycoprotein staining and proteinase and hyaluronidase substrate zymographic profiles. The results have shown quantitative and qualitative differences in 1‐DE protein and glycoprotein profiles with respect to the employed isolation approach. These differences were seen even more clearly in 2‐DE protein profiles, where it was possible to distinguish the presence/absence, changes in relative abundance and pI/M_r shifts of various protein spots. Proteinase and hyaluronidase zymograms supported the prediction that various isolation protocols result in various profiles of enzymatically active molecules.     

Maximum Saccharification of Cellulose Complex by an Enzyme Cocktail Supplemented with Cellulase from Newly Isolated <Emphasis Type="BoldItalic">Aspergillus fumigatus</Emphasis> ECU0811

Either the natural biodegradation process or the industrial hydrolytic process requires synergistic interactions between various cellulases. However, it is sometimes impeded by low hydrolytic rate of existing cellulases and the lack of accessory enzymes. Herein, the ability of a commercial cellulase (Spezyme CP, from Genencor) to degrade steam explosion-pretreated corn stover was significantly improved. Firstly, a fungal cellulase producer, Aspergillus fumigatus ECU0811, was isolated from hundreds of soil samples. A 96-deep-well microscale-based platform was developed here to reduce the labor-intensive screening work and proved to be consistent with macroscale screening work. After optimization of fermentation, 3% corn cob could induce A. fumigatus ECU0811 to yield the highest cellulase production. Based on the high activities of β-glucosidase and xylanase by A. fumigatus ECU0811, 0.91 and 125 U/mg protein, respectively, an enzyme cocktail was composed with a fixed dosage of Spezyme CP (CPCel) at 14.2 filter paper units (FPU)/g glucan and varied dosages of A. fumigatus cellulase (AFCel). Consequently, the glucan-to-glucose conversion of corn stover was increased from 25.6% in the presence of CPCel at a dosage of 14.2 FPU/g glucan to 99.5% in the presence of the enzyme cocktail (14.2 FPU CPCel plus 1.21 FPU AFCel per gram of glucan). On the other side, it reduced the total protein amount of CPCel by as much as tenfold, which extremely improved the hydrolytic rate of Spezyme CP and reduced its dosage.     

Secretome of the preimplantation human embryo by bottom-up label-free proteomics

A bottom-up label-free mass spectrometric proteomic strategy was used to analyse the protein profiles of the human embryonic secretome. Culture media samples used for embryonic culture of patients undergoing intracytoplasmic sperm injection cycles were selected as a test case for this exploratory proof-of-principle study. The media were stored after embryo transfer and then pooled into positive (n = 8) and negative (n = 8) implantation groups. The absolute quantitative bottom-up technique employed a multidimensional protein identification technology based on separation by nano-ultra-high pressure chromatography and identification via tandem nano-electrospray ionization mass spectrometry with data-independent scanning in a hydrid QqTOF mass spectrometer. By applying quantitative bottom-up proteomics, unique proteins were found exclusively in both the positive- and negative-implantation groups, which suggest that competent embryos express and secrete unique biomarker proteins into the surrounding culture medium. The selective monitoring of these possible secretome biomarkers could make viable procedures using single-embryo transfer.     

2DE‐based approach for estimation of number of protein species in a cell

Insufficient sensitivity of methods for detection of proteins at a single molecule level does not yet allow obtaining the whole image of human proteome. But to go further, we need at least to know the proteome size, or how many different protein species compose this proteome. This is the task that could be at least partially realized by the method described in this article. The approach used in our study is based on detection of protein spots in 2DE after staining by protein dyes with various sensitivities. As the different protein spots contain different protein species, counting the spots opens a way for estimation of number of protein species. The function representing the dependence of the number of protein spots on sensitivity or LOD of protein dyes was generated. And extrapolation of this function curve to theoretical point of the maximum sensitivity (detection of a single smallest polypeptide) allowed to counting the number of different molecules (polypeptide species) at the concentration level of a single polypeptide per proteome. Using this approach, it was estimated that the minimal numbers of protein species for model objects, Escherichia coli and Pirococcus furiosus, are 6200 and 3400, respectively. We expect a single human cell (HepG2) to contain minimum 70 000 protein species.     

Effects of active silicon uptake by rice on 29Si fractionation in various plant parts

Rice (Oryza sativa L.) accumulates large amounts of silicon which improves its growth and health due to enhanced resistance to biotic and abiotic stresses. Silicon uptake and loading to xylem in rice are predominantly active processes performed by transporters encoded by the recently identified genes Lsi1 (Si influx transporter gene) and Lsi2 (Si efflux transporter gene). Silicon deposition in rice during translocation to upper plant tissues is known to discriminate against the heavier isotopes ²⁹Si and ³⁰Si, resulting in isotope fractionation within the plant. We analyzed straw and husk samples of rice mutants defective in Lsi1, Lsi2 or both for silicon content and δ²⁹Si using isotope ratio mass spectrometry (IRMS) and compared these results with those for the corresponding wild‐type varieties (WT). The silicon content was higher in husk than in straw. All the mutant rice lines showed clearly lower silicon content than the WT lines (4–23% Si of WT). The δ²⁹Si was lower in straw and husk for the uptake defective mutant (lsi1) than for WT, albeit δ²⁹Si was 0.3‰ higher in husk than in straw in both lines. The effect of defective efflux (lsi2) differed for straw and husk with higher δ²⁹Si in straw, but lower δ²⁹Si in husk while WT showed similar δ²⁹Si in both fractions. These initial results show the potential of Si isotopes to enlighten the influence of active uptake on translocation and deposition processes in the plant. Copyright © 2009 John Wiley & Sons, Ltd.     

Improved Treatment and Utilization of Rice Straw by <Emphasis Type="Italic">Coprinopsis cinerea</Emphasis>

As one of the most abundant renewable resources, rice straw is an attractive lignocellulosic material for animal feeding or for the production of biochemical. An appropriate pre-treatment technique is essential for converting rice straw to rich fodder or biofuel. Based on previous work, Coprinopsis cinerea can grow on rice straw medium and therefore it is useful for the treatment of rice straw. However, little is known regarding its degradation systems and nutrition values. In this study, we firstly found that C. cinerea could grow rapidly on rice straw without any additives by the production of a series of enzymes (laccase, cellulase, and xylanase) and that the microstructure and contents of rice straw changed significantly after being treated by C. cinerea. We propose that a possible underlying mechanism exists in the degradation. Moreover, C. cinerea has a high nutrition value (23.5% crude protein and 22.2% total amino acids). Hence, fermented rice straw with mycelium could be a good animal feedstuff resource instead of expensive forage. The direct usage of C. cinerea treatment is expected to be a practical, cost-effective, and environmental-friendly approach for enhancing the nutritive value and digestibility of rice straw.     

Solid-state fermentation of agricultural wastes into food through pleurotus cultivation

The technical feasibility of using agricultural wastes (mango and date industry wastes) as a substrate for the cultivation ofPleurotus ostreatus NRRL-0366 is evaluated. When comparing the biological efficiency of mushroom production, the highest yield of fruiting bodies was obtained using a mixture of date waste and rice straw at a ratio (1:1) (11.96%), followed by a mixture 3:1 (11.16%). The lowest one was the mixture 2:1 (9.19%). FungusPleurotus ostreatus NRRL-0366 can also be cultivated on mango waste supplemented with rice straw at a different ratio. The best one was the 1:1 mixture (10.18%), whereas the lowest was a mixture 3:1 (6.4%). Comparing the results obtained favored the use of date waste as a substrate for growingPleurotus ostreatus NRRL-0366. Spawn was cultured on three different substrates as follows: Date waste alone (I); 1:1 (by wt) date waste and rice straw (II); 1:1:1 date waste, rice straw, and corncobs (III). Final dry weight and composition of the fruiting bodies are tabulated for the three sets of conditions. Date waste and rice straw mixture (II) is a good source of nonstarchy carbohydrate (67%) and protein (27.44%) containing amounts of essential amino acids, especially lysine and low RNA (3.81%). Elemental analysis were studied in the fruit bodies of the three media.     

Effective protein extraction protocol for proteomics studies of Jerusalem artichoke leaves

Protein extraction is a crucial step for proteomics studies. To establish an effective protein extraction protocol suitable for two‐dimensional electrophoresis (2DE) analysis in Jerusalem artichoke (Helianthus tuberosus L.), three different protein extraction methods—trichloroacetic acid/acetone, Mg/NP‐40, and phenol/ammonium acetate—were evaluated using Jerusalem artichoke leaves as source materials. Of the three methods, trichloroacetic acid/acetone yielded the best protein separation pattern and highest number of protein spots in 2DE analysis. Proteins highly abundant in leaves, such as Rubisco, are typically problematic during leaf 2DE analysis, however, and this disadvantage was evident using trichloroacetic acid/acetone. To reduce the influence of abundant proteins on the detection of low‐abundance proteins, we optimized the trichloroacetic acid/acetone method by incorporating a PEG fractionation approach. After optimization, 363 additional (36.2%) protein spots were detected on the 2DE gel. Our results suggest that trichloroacetic acid/acetone method is a better protein extraction technique than Mg/NP‐40 and phenol/ammonium acetate in Jerusalem artichoke leaf 2DE analysis, and that trichloroacetic acid/acetone method combined with PEG fractionation procedure is the most effective approach for leaf 2DE analysis of Jerusalem artichoke.     

Concentration and pattern changes of porcine serum apolipoprotein A‐I in four different infectious diseases

Apolipoprotein A‐I (Apo A‐I) is a major protein in lipid/lipoprotein metabolism and decreased serum levels have been observed in many species in response to inflammatory and infectious challenges. Little is known about the porcine homologue, therefore in this work we have characterized it through biochemical and proteomic techniques. In 2DE, porcine serum Apo A‐I is found as three spots, the two more acidic ones corresponding to the mature protein, the more basic spot to the protein precursor. Despite high sequence coverage in LC‐MS/MS, we did not find a sequence or PTM difference between the two mature protein species. Besides this biochemical characterization, we measured overall levels and relative species abundance of serum Apo A‐I in four different viral and bacterial porcine infectious diseases. Lower overall amounts of Apo A‐I were observed in Salmonella typhimurium and Escherichia coli infections. In the 2DE protein pattern, an increase of the protein precursor together with a lower level of mature protein species were detected in the porcine circovirus type 2‐systemic disease and S. typhimurium infection. These results reveal that both the porcine serum Apo A‐I concentration and the species pattern are influenced by the nature of the infectious disease.     

Comparative analysis of prostate‐specific antigen by two‐dimensional gel electrophoresis and capillary electrophoresis

Serum levels of Prostate‐Specific Antigen (PSA) are not fully specific for prostate cancer (PCa) diagnosis and several efforts are focused on searching to improve PCa markers through the study of PSA subforms that could be cancer associated. We have previously reported by 2DE a decrease in the sialic acid content of PSA from PCa compared to benign prostatic hyperplasia patients based on the different proportion of the PSA spots. However, faster and more quantitative techniques, easier to automate than 2DE, are desirable. In this study, we examined the potential of CE for resolving PSA subforms in different samples and compared the results with those obtained by 2DE. We first fractionated by OFFGEL the subforms of PSA from seminal plasma according to their pI s and analyzed each separated fraction by 2DE and CE. We also analyzed PSA and high pI PSA, both from seminal plasma, and PSA from urine of a PCa patient. These samples with different PSA spots proportions by 2DE, due to different posttranslational modifications, also presented different CE profiles. This study shows that CE is a useful and complementary technique to 2DE for analyzing samples with different PSA subforms, which is of high clinical interest.     

An immunoproteomic approach for characterization of the outer membrane proteins of Salmonella Gallinarum

Salmonella enterica serovar Gallinarum (SG) is an important pathogen that causes fowl typhoid in chickens. In order to investigate SG outer membrane proteins (OMPs) as potential vaccine candidate proteins, we established a proteomic map and database of antigenic SG‐OMPs. A total of 174 spots were detected by 2DE. Twenty‐two antigen‐reactive spots were identified as nine specific proteins using PMF. OmpA was the most abundant protein among all of the identified OMPs, and it exhibited seven protein species. We conducted Western blot analysis for the SG‐OMPs in order to determine which proteins were cross‐reactive to the serovars Salmonella Enteritidis, Salmonella Typhimurium, and SG. Our results indicated that OmpA was considered to be an antigenic cross‐reactive protein among the three serovars. This study sheds new light on our understanding of cross‐protection among Salmonella serovars.     

Evaluation of extraction procedures for 2‐DE analysis of aphid proteins

Protein sample preparation is a crucial step in a 2‐DE proteomics approach. In order to establish a routine protocol for the application of proteomics analysis to aphids, this study focuses on the specific protein extraction problems in insect tissues and evaluates four methods to bypass them. The approaches of phenol extraction methanol/ammonium acetate precipitation (PA), TCA/acetone precipitation, PEG precipitation, and no precipitation were evaluated for proteins isolation and purification from apterous adult aphids, Sitobion avenae. For 2‐DE, the PA protocol was optimal, resulting in good IEF and clear spots. PA method yielded the greatest amount of protein and displayed most protein spots in 2‐DE gels, as compared with the TCA/acetone precipitation, PEG precipitation and no precipitation protocols. Analysis of protein yield, image quality and spot numbers demonstrate that the TCA/acetone precipitation protocol is a reproducible and reliable method for extracting proteins from aphids. The PEG precipitation approach is a newly developed protein extraction protocol for aphids, from which more unique protein spots can be detected, especially for detection of acid proteins. These protocols are expected to be applicable to other insects or could be of interest to laboratories involved in insect proteomics, despite the amounts and types of interfering compounds vary considerably in different insects.     

Simultaneous determination of sulfoxaflor and its metabolites,X11719474 and X11721061, in brown rice and rice straw after field application using LC-MS/MS

The present study was carried out to develop an analytical method for simultaneously detecting and quantifying sulfoxaflor and its metabolites (X11721061, X11719474) in brown rice and rice straw using liquid chromatography–tandem mass spectrometry. The parent compound and its metabolites were extracted and purified using original ‘QuEChERS’ method with modification. The matrix-matched calibration curve of sulfoxaflor and its metabolites in both matrices achieved good linearity with determination coefficients (R²) ≥0.9944. The overall recoveries of sulfoxaflor at two fortification levels (rice: 0.2 and 1.0 mg/kg; rice straw: 0.4 and 2.0 mg/kg) ranged from 97.37% to 107.71% with relative standard deviations (RSDs) <5%. On the other hand, the recoveries of both metabolites (X11721061 and X11719474) at 0.1 and 0.5 mg/kg (rice) and 0.2 and 1.0 mg/kg (rice straw) were satisfactory with values ranging from 83.70 % to 112.60% with RSDs <8%. During storage at ?20°C, the analyte and its metabolites were stable for up to 87 days. The limits of quantification of 0.02 mg/kg were lower than the maximum residue limit (0.2 mg/kg) set by the Korean Ministry of Food and Drug Safety for brown rice. The method was successfully applied to paddy field treated with different programme schedules and a preharvest interval of 7 days was proposed based upon the current study. In sum, the developed method is accurate and reproducible for ensuring the reliable determination of sulfoxaflor (and its metabolites) in harvested rice grain and straw samples from the field. The residual level of parent compound does not seem to pose any hazardous effect and treated rice could be safely used for consumption.     

Combination of virtual and experimental 2DE together with ESI LC‐MS/MS gives a clearer view about proteomes of human cells and plasma

Virtual and experimental 2DE coupled with ESI LC‐MS/MS was introduced to obtain better representation of the information about human proteome. The proteins from HEPG2 cells and human blood plasma were run by 2DE. After staining and protein spot identification by MALDI‐TOF MS, the protein maps were generated. The experimental physicochemical parameters (pI/Mw) of the proteoforms further detected by ESI LC‐MS/MS in these spots were obtained. Next, the theoretical pI and Mw of identified proteins were calculated using program Compute pI/Mw ( http://web.expasy.org/compute_pi/pi_tool‐doc.html ). Accordingly, the relationship between theoretical and experimental parameters was analyzed, and the correlation plots were built. Additionally, virtual/experimental information about different protein species/proteoforms from the same genes was extracted. As it was revealed from the plots, the major proteoforms detected in HepG2 cell line have pI/Mw parameters similar to theoretical values. In opposite, the minor protein species have mainly very different from theoretical pI and Mw parameters. A similar situation was observed in plasma in much higher degree. It means that minor protein species are heavily modified in cell and even more in plasma proteome.