MALDI‐TOF MS identification of microbiota associated with pest insect Diabrotica speciosa

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Bom m 9 from Bombyx mori is a novel protein related to asthma

The silkworm (Bombyx mori) can cause severe IgE‐mediated allergic disease, however, the mechanism remains unclear. The aim of this study was to investigate the immunologic mechanism by which silkworms induce allergy. Whole silkworm pupa proteins were separated by SDS‐PAGE and 2‐D PAGE. Then, IgE‐binding proteins were detected by immunoblotting with sera of patients having an allergy to Bombyx mori. After tryptic digestion, the peptides of IgE‐binding proteins were analyzed by matrix‐assisted laser desorption ionization tandem time‐of‐flight mass spectrometry or tandem mass spectrometry. Database searches were used to identify allergens in silkworm pupa, after which Bom m 9 was to construct an asthma model. Thus, in the current study, a mouse asthma model was constructed with Bom m 9.     

Defensin‐like peptide3 from black solder fly: Identification,characterization, and key amino acids for anti‐Gram‐negative bacteria

An antibacterial peptide was isolated from a black soldier fly, Hermetia illucens. The molecular mass of this peptide was established as 4247.37 by matrix‐assisted laser desorption/ionization‐time of flight mass (MALD‐TOF MS) spectrometry. The amino acid sequence of the mature peptide was determined by N‐terminal sequencing using Edman degradation, combined with cDNA sequencing of the previously reported defensin‐like peptide (DLP) 3. Analysis of the minimal inhibitory concentration (MIC) revealed that DLP3 had potent activity against Gram‐positive and negative bacteria, but DLP4 had only anti‐Gram‐positive activity as previously reported. Recombinant DLP3 and DLP4 were overexpressed in Escherichia coli, and antibacterial activities were identical to DLPs purified from H. illucens hemolyph. In silico analysis revealed that only six amino acid sequences were different between DLP3 and DLP4, but antibacterial activity against Gram‐negative bacteria differed. Therefore these amino acid variants may be key amino acids (Gly‐10, Val‐18, Met‐23, Arg‐25, Asp‐32, Arg‐40) related to killing Gram‐negative bacteria.     

Proteomic analysis of the venom of the predatory ant Pachycondyla striata (Hymenoptera: Formicidae)

The ants use their venom for predation, defense, and communication. The venom of these insects is rich in peptides and proteins, and compared with other animal venoms, ant venoms remain poorly explored. The objective of this study was to evaluate the protein content of the venom in the Ponerinae ant Pachycondyla striata. Venom samples were collected by manual gland reservoir dissection, and samples were submitted to two‐dimensional gel electrophoresis and separation by ion‐exchange and reverse‐phase high‐performance liquid chromatography followed by mass spectrometry using tanden matrix‐assisted laser desorption/ionization with time‐of‐flight (MALDI‐TOF/TOF) mass spectrometry and electrospray ionization‐quadrupole with time‐of‐flight (ESI‐Q/TOF) mass spectrometry for obtaining amino acid sequence. Spectra obtained were searched against the NCBInr and SwissProt database. Additional analysis was performed using PEAKS Studio 7.0 (Sequencing de novo). The venom of P. striata has a complex mixture of proteins from which 43 were identified. Within the identified proteins are classical venom proteins (phospholipase A, hyaluronidase, and aminopeptidase N), allergenic proteins (different venom allergens), and bioactive peptides (U10‐ctenitoxin Pn1a). Venom allergens are among the most expressed proteins, suggesting that P. striata venom has high allergenic potential. This study discusses the possible functions of the proteins identified in the venom of P. striata.     

Comparative Analysis of the Endosperm Proteins Separated by 2-D Electrophoresis for Two Cultivars of Hybrid Rice （Oryza sativa L,）

Liangyoupeijiu is a two-parental-line, and Shanyou63 is a three-parental-line hybrid rice （Oryza sativa L.）. Although both belong to the indica subspecies, they have obvious differences with respect to morphology, physiology and grain quality. Variations in endosperm protein compositions were studied by comparing the 2-D electrophoresis （2-DE） maps for these two cultivars of hybrid rice. After matrix-assisted laser desorption/ionization time of flight mass spectrometry （MALDI-TOF/MS） analysis, a 21-kDa precursor of 19- kDa globulin was identified as the major storage protein for both cultivars. Some isoforms of peroxiredoxin and seed maturation protein were found to only exist in Shanyou63, whereas aldose reductase and starch granule-bound starch synthase were only detected in Liangyoupeijiu. These data might provide a foundation for further comparative studies of these two cultivars of hybrid rice.     

C-terminal sequencing by mass spectrometry: application to gelatine-derived proline-rich peptides

Protonated peptides derived from proline‐rich proteins (PRP) are often difficult to sequence by standard collision‐induced dissociation (CID) mass spectrometry (MS) due to preferential amide bond cleavage N‐terminal to proline. In connection with bovine spongiform encephalopathy regulations, proteolytic products derived from the PRP collagen have been suggested as markers for contamination of animal feedstuffs with processed animal protein (Fernandez Ocaña, M. et al., Analyst 2004, 129, 111–115). Herein, we report the identification of these marker peptides using the strategy of C‐terminal sequencing by CID MS from their sodium and lithium adducts. Upon fragmentation a new cationized peptide was produced that is one C‐terminal amino acid shorter in length. This dissociation pathway allowed for the facile identification of the C‐terminal residue by matrix‐assisted laser desorption/ionization tandem time‐of‐flight mass spectrometry. Each newly formed cationized peptide was further fragmented by up to seven stages of electrospray ionization ion trap MS. Proline‐rich C‐terminal sequence tags were established which permitted successful database identification of collagen alpha type I proteins.     

Culture conditions and sample preparation methods affect spectrum quality and reproducibility during profiling of Staphylococcus aureus with matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry

Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) has emerged as a promising tool to rapidly characterize Staphylococcus aureus. Different protocols have been employed, but effects of experimental factors, such as culture condition and sample preparation, on spectrum quality and reproducibility have not been rigorously examined. We applied MALDI‐TOF MS to characterize a model system consisting of five methicillin‐sensitive (MSSA) and five methicillin‐resistant S. aureus isolates (MRSA) under two culture conditions (agar and broth) and using two sample preparation methods [intact cell method and protein extraction method (PEM)]. The effects of these treatments on spectrum quality and reproducibility were quantified. PEM facilitated increases in the number of peaks and mass range width. Broth cultures further improved spectrum quality in terms of increasing the number of peaks. In addition, PEM increased reproducibility in samples prepared using identical culture conditions. MALDI imaging data suggested that the improvement in reproducibility may result from a more homogeneous distribution of sample associated with the broth/PEM treatment. Broth/PEM treatment also yielded the highest rate (96%) of correct classification for MRSA. Taken together, these results suggest that broth/PEM maximizes the performance of MALDI‐TOF MS to characterize S. aureus.

Significance and Impact of the Study

Two culture conditions (agar or broth) and two sample preparation methods (intact cell or protein extraction) were evaluated for their effects on profiling of Staphylococcus aureus using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS). Results indicated that MALDI‐enabled profiling of S. aureus is most effective when cultures are grown in broth and processed using a protein extraction‐based approach. These findings should enhance future efforts to maximize the performance of this approach to characterize strains of S. aureus.     

Novel short antimicrobial peptide isolated from Xenopus laevis skin

A rich source of bioactive peptides, including a large number of antimicrobial peptides, has been found in amphibian skin. In this study, a novel short antimicrobial peptide was purified from Xenopus laevis skin and characterised through reversed‐phase high‐performance liquid chromatography, Edman degradation and matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry. The peptide was composed of six amino acids with a sequence of DEDLDE and thus named X. laevis antibacterial peptide‐P2 (XLAsp‐P2). Transmission electron microscopy revealed that this peptide showed potential antimicrobial abilities against bacteria by damaging the bacterial cell membrane. XLAsp‐P2 maybe inhibit bacterial growth by binding to the microbial genomic DNA. The peptide also exhibited a weak haemolytic activity against rabbit red blood cells. Therefore, XLAsp‐P2 is a novel short anionic antibacterial peptide with broad activities. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.     

Purification and characterization of a D‐mannose specific lectin from the green marine alga,Bryopsis plumosa

A d ‐mannose specific lectin was purified from the green marine alga, Bryopsis plumosa (Huds.) Ag. The lectin agglutinated horse and sheep erythrocytes. Matrix assisted laser desorption/ionization time of flight mass spectrometry, size exclusion chromatography, sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) and two dimensional gel electrophoresis (2DE) results showed that the lectin was a monomer with molecular weight of 17 kDa and pI 7.3. The agglutinating activity was inhibited by d ‐mannose (1 mM), α‐methyl‐D‐mannose (4 mM) and l ‐fucose (8 mM). d ‐glucose (125 mM) showed weak inhibition. The lectin did not need divalent cations for agglutinating activity. N‐terminal amino acid sequence of the lectin was analyzed. As the lectin was novel, we named it BPL‐2 (Bryopsis plumosa lectin 2). Full cDNA sequence of BPL‐2 was obtained using cDNA library. It was comprised of 624 bp of open reading frame and 167 bp/57 bp of 3′/5′ untranslated regions as well as N‐terminal signal peptide. No antimicrobial activity of BPL‐2 was observed in four bacteria strains tested.     

Cell‐bound exopolysaccharide from probiotic bacteria induces autophagic cell death of tumour cells

Aim: Lactic acid bacteria (LAB) are beneficial micro‐organisms that have been associated with several probiotic effects in both humans and animals. Here, using proteome analysis, we investigate the antitumour effects of cell‐bound exopolysaccharides (cb‐EPS) isolated from Lactobacillus acidophilus 606 on colon cancer cells and explore the proteins critical for their antitumour activity. Methods and Results: cb‐EPS inhibited the proliferation of HT‐29 colon cancer cells by directly affecting cell morphology and not the cell cycle. Using two‐dimensional polyacrylamide gel electrophoresis coupled with matrix‐assisted laser desorption‐ionization time‐of‐flight mass spectrometry (MALDI‐TOF/MS) and immunoblot analysis, we found that cb‐EPS dramatically induced Beclin‐1 and GRP78, and affected Bcl‐2 and Bak regulation. Conclusions: The results of this study indicate that cb‐EPS are antitumourigenic against HT‐29 colon cancer cells and that this activity is because of the activation of autophagic cell death promoted directly by the induction of Beclin‐1 and GRP78, as well as indirectly through the induction of Bcl‐2 and Bak. Significance and Impact of the Study: These results may contribute to understanding the novel mechanisms by which probiotic bacteria induce tumour cell death via autophagy.     

Proteomic analysis of the immune response of the silkworm infected by Escherichia coli and Bacillus bombyseptieus

Abstract The silkworm, Bombyx mori, is an economically important insect with a 5 000‐year history of domestication. During evolution, the silkworm has developed highly effective defenses against invasion and parasitization by microorganisms. In this study, two microorganisms Escherichia coli and Bacillus bombyseptieus were orally infected to silkworm larvae. After infection with E. coli and B. bombyseptieus for 24 h, we investigated the polypeptide changes in the hemolymph, midgut and integument using two‐dimensional gel electrophoresis and matrix‐assisted laser desorption ionization time of flight mass spectrometry. Forty‐seven differentially expressed proteins were identified in these tissues. They belonged to a variety of functional classes, including immune proteins, metabolic proteins and structural proteins. Compared with controls, E. coli‐infected silkworms showed 21 up‐regulated proteins, 25 down‐regulated proteins and lost one protein. After infection with B. bombyseptieus, silkworms showed 15 up‐regulated proteins, 27 down‐regulated proteins, lost three proteins and retained two proteins unchanged. We speculate that all these proteins may play a role in the silkworm immune response, although it is unclear why and how the two kinds of bacteria can so markedly alter expression of these proteins. These results offer valuable insights for measuring the proteomic responses of the silkworm innate immune mechanism.     

Filamentous fungal characterizations by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry

Matrix‐assisted laser desorption/ionization time‐of‐flight intact cell mass spectrometry (MALDI‐TOF ICMS) is coming of age for the identification and characterization of fungi. The procedure has been used extensively with bacteria. UV‐absorbing matrices function as energy mediators that transfer the absorbed photoenergy from an irradiation source to the surrounding sample molecules, resulting in minimum fragmentation. A surprisingly high number of fungal groups have been studied: (i) the terverticillate penicillia, (ii) aflatoxigenic, black and other aspergilli, (iii) Fusarium, (iv) Trichoderma, (iv) wood rotting fungi (e.g. Serpula lacrymans) and (v) dermatophytes. The technique has been suggested for optimizing quality control of fungal Chinese medicines (e.g. Cordyceps). MALDI‐TOF ICMS offers advantages over PCR. The method is now used in taxonomic assessments (e.g. Trichoderma) as distinct from only strain characterization. Low and high molecular mass natural products (e.g. peptaibols) can be analysed. The procedure is rapid and requires minimal pretreatment. However, issues of reproducibility need to be addressed further in terms of strains of species tested and between run variability. More studies into the capabilities of MALDI‐TOF ICMS to identify fungi are required.     

Proteomic analysis of tilapia Oreochromis niloticus Streptococcus agalactiae strains with different genotypes and serotypes

Nine tilapia Oreochromis niloticus group B streptococcus (GBS) strains differing in serotype and genotype were selected and paired. Two‐dimensional difference gel electrophoresis (2D DIGE) and matrix‐assisted laser‐desorption ionization time‐of‐flight‐mass spectrometry (MALDI‐TOF‐MS) were used to analyse the protein profiles of the strain pairs. Forty‐three proteins corresponding to 66 spots were identified, of which 35 proteins were found in the seven selected strain pairs that represented pairs differing in genotype and serotype. Among the 35 proteins, numbers of differentially expressed proteins in strains of different serotypes were greater than found in strains of different genotypes, suggesting that serotype plays a more essential role than genotype in the differential protein expression among GBS strains. No distinct pattern was found with respect to genotype and the protein expression profile of GBS strains. Several proteins were identified as surface‐associated cytoplasmic proteins that possessed the typical immunity‐eliciting characteristics of surface proteins. The identified proteins were found to be involved in 16 biological processes and seven Kyoto encyclopaedia of genes and genomes (KEGG) pathways. The data, for the first time, identified differentially expressed proteins in O. niloticus GBS strains of different serotypes, which play a major role in immunogenicity of O. niloticus GBS than does genotype, offering further information for design of a vaccine against O. niloticus GBS.     

Synthesis and matrix assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry study of phosphopeptide

Summary The symmetry phosphoramidite reagents were synthesized via a two-step route and used for the ‘one pot’ synthesis of the phosphoserine building block Fmoc-Ser(PO(OBzl)OH)-OH. The procedure is simple and rapid, and product is obtained in high yield. When using this building block, the phosphopeptide (RKGS(PO₃H₂)SSNEPSSDSLSSPTLLAL) related to the C-terminal of c-Fos protein was synthesized manually by Fmoc/t-Bu procedure and characterized by matrix assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry. In the fragment ion of phosphopeptide in the MALDI-TOF mass spectrometry with a curved field reflection, the acquired information can be used to identify the sequences and the phosphorylation sites of the peptide.     

Role of estrogenic compounds (diethylstibestrol, 17β‐estradiol,and bisphenol A) in the phosphorylation of substrate by protein kinase Cα

Estrogenic compounds can activate protein kinase C (PKC), which is a calcium and phospholipid‐dependent serine/threonine kinase. In the present study, we investigated the role of 17β‐estradiol (E2), diethylstibestrol (DES), and bisphenol A (BPA) in the phosphorylation of substrate by PKCα using the matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry. The level of phosphorylated peptide was low in the absence of phosphatidylserine (PS). Moreover, reduction of phosphorylation ratios was identified in the presence of diacylglycerol (DAG) and Ca²⁺ or PS and Ca²⁺ after adding E2, DES, and BPA. However, no change in phosphorylation ratios was found in the presence of DAG and PS. Addition of E2, DES, and BPA also had no influence on the phosphorylation reaction of substrate by cell or tissue lysate samples. Our study suggests that E2, DES, and BPA can bind to the C2 domain of PKCα but have no effects on the phosphorylation reaction of substrates in the presence of DAG and PS. © 2009 Wiley Periodicals, Inc. J Biochem Mol Toxicol 23:318–323, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20294     

Proteomic profiling of the hemolymph at the fifth instar of the silkworm Bombyx mori

Abstract Two‐dimensional gel electrophoresis (2‐DE) followed by matrix‐assisted laser desorption ionization – time‐of‐flight/time‐of‐flight mass spectrometry (MS) analysis were used to charaterize the hemolymph proteomic profiles of the silkworm, Bombyx mori. At days 4 (V4) and 5 (V5) of the fifth (final) instar, when the larvae were at the fast‐growing stage, we found dramatic changes in spots representing proteins having an approximate molecular weight (MW) of 30 kDa. Of these spots, four 30K proteins were highly up‐regulated, implying a close association with the growth and development of B. mori larvae. To understand the molecular basis and underlying mechanisms involved in development and metamorphosis, the proteome of whole hemolymph at V5 was analyzed using shotgun liquid chromatography tandem mass spectrometry with an LTQ‐Orbitrap. A total of 108 proteins were identified without any false discovery hits. These proteins were involved in a variety of cellular functions, including metabolism, development, nutrient transport and reserve, and defense response. Gene ontology analysis showed that 3.4% of these proteins had nutrient reservoir activities and 5.7% were involved in the response to stimulus. Pathway analysis revealed that 22 proteins with common targets were involved in various cellular processes such as immunity, differentiation, proliferation and metamorphosis. These results suggested that some key factors such as the 30K proteins in hemolymph play important roles in B. mori growth and development. Moreover, the multiple functions of hemolymph may be operated by a complex biological network.     

Quantification of plant surface metabolites by matrix‐assisted laser desorption–ionization mass spectrometry imaging: glucosinolates on Arabidopsis thaliana leaves

The localization of metabolites on plant surfaces has been problematic because of the limitations of current methodologies. Attempts to localize glucosinolates, the sulfur‐rich defense compounds of the order Brassicales, on leaf surfaces have given many contradictory results depending on the method employed. Here we developed a matrix‐assisted laser desorption–ionization (MALDI) mass spectrometry protocol to detect surface glucosinolates on Arabidopsis thaliana leaves by applying the MALDI matrix through sublimation. Quantification was accomplished by spotting glucosinolate standards directly on the leaf surface. The A. thaliana leaf surface was found to contain approximately 15 nmol of total glucosinolate per leaf with about 50 pmol mm^?2 on abaxial (bottom) surfaces and 15–30 times less on adaxial (top) surfaces. Of the major compounds detected, 4‐methylsulfinylbutylglucosinolate, indol‐3‐ylmethylglucosinolate, and 8‐methylsulfinyloctylglucosinolate were also major components of the leaf interior, but the second most abundant glucosinolate on the surface, 4‐methylthiobutylglucosinolate, was only a trace component of the interior. Distribution on the surface was relatively uniform in contrast to the interior, where glucosinolates were distributed more abundantly in the midrib and periphery than the rest of the leaf. These results were confirmed by two other mass spectrometry‐based techniques, laser ablation electrospray ionization and liquid extraction surface analysis. The concentrations of glucosinolates on A. thaliana leaf surfaces were found to be sufficient to attract the specialist feeding lepidopterans Plutella xylostella and Pieris rapae for oviposition. The methods employed here should be easily applied to other plant species and metabolites.     

Detection of Biomarkers of Pathogenic Naegleria fowleri Through Mass Spectrometry and Proteomics

Emerging methods based on mass spectrometry (MS) can be used in the rapid identification of microorganisms. Thus far, these practical and rapidly evolving methods have mainly been applied to characterize prokaryotes. We applied matrix‐assisted laser‐desorption‐ionization‐time‐of‐flight mass spectrometry MALDI‐TOF MS in the analysis of whole cells of 18 N. fowleri isolates belonging to three genotypes. Fourteen originated from the cerebrospinal fluid or brain tissue of primary amoebic meningoencephalitis patients and four originated from water samples of hot springs, rivers, lakes or municipal water supplies. Whole Naegleria trophozoites grown in axenic cultures were washed and mixed with MALDI matrix. Mass spectra were acquired with a 4700 TOF‐TOF instrument. MALDI‐TOF MS yielded consistent patterns for all isolates examined. Using a combination of novel data processing methods for visual peak comparison, statistical analysis and proteomics database searching we were able to detect several biomarkers that can differentiate all species and isolates studied, along with common biomarkers for all N. fowleri isolates. Naegleria fowleri could be easily separated from other species within the genus Naegleria. A number of peaks detected were tentatively identified. MALDI‐TOF MS fingerprinting is a rapid, reproducible, high‐throughput alternative method for identifying Naegleria isolates. This method has potential for studying eukaryotic agents.