Peptide Mass Research Articles

Partial characterization of purified glycoprotein from nutshell of Arachis hypogea L. towards macrophage activation and leishmaniacidal activity.

Arachis hypogea L. protein fraction-2 (AHP-F2) from the Peanut shell was extracted and characterized and its potent immunomodulatory and anti-leishmanial role was determined in this present study. AHP-F2 was found to be a glycoprotein as the presence of carbohydrates were confirmed by the analysis of high-performance liquid chromatography (HPLC) yielded glucose, galactose, mannose, and xylose. AHP-F2 molecular mass was found to be ∼28kDa as indicated in MALDI-TOF and peptide mass fingerprinting analysis followed by Mascot search. The peptide matches revealed the similarity of the mannose/glucose binding lectin with 71.07% in the BLAST analysis. After that, the 3D structure of the AHP-F2 model was designed and validated by the Ramachandran plot. The immunomodulatory role of AHP-F2 was established in murine peritoneal macrophages as induction of nitric oxide (NO), and stimulation of proinflammatory cytokines (IL-12 and IFN-γ) in a dose-dependent manner was observed. Interestingly, it was also found that AHP-F2 has interacted with the innate immune receptor, toll-like receptors (TLRs) as established in molecular docking as well as mRNA expression. The anti-leishmanial potential of AHP-F2 was revealed with a prominent inhibition of amastigote growth within the murine macrophages with prompt induction of nitrite release. Altogether, the isolated AHP-F2 from Arachis hypogea L. has strong immunomodulatory and anti-leishmanial potential which may disclose a new path to treat leishmaniasis.

Active Whaling, Opportunistic Scavenging or Long-Distance Trading: Zooarchaeological, Palaeoproteomic, and Historical Analyses on Whale Exploitation and Bone Working in Anglo-Saxon Hamwic

THE ANGLO-SAXON SITE OF HAMWIC (modern Southampton, Hampshire, UK) has been identified as a major bone-working centre. Besides antler and terrestrial mammal bone, cetacean bone has been recovered in high quantities. These specimens primarily represent working waste. Using peptide mass fingerprinting of bone collagen (ZooMS), it was determined that the majority of these specimens derive from the currently highly endangered population of North Atlantic right whale (Eubalaena glacialis). Limited historical sources appear to suggest that whaling was undertaken by the Anglo-Saxons, or by the Normans on the other side of the English Channel prior to the eleventh century ad. Nevertheless, the primary method of acquisition for whale bone was through opportunistic scavenging and trading.

Charting and tracking the evolution of the SARS CoV-2 coronavirus variants of concern with protein mass spectrometry.

The evolution of the SARS-CoV2 coronavirus spike S-protein is studied using a mass spectrometry based protein phylogenetic approach. A study of a large dataset comprising sets of peptide masses derived from over 3000 proteins of the SARS-CoV2 virus shows that the approach is capable of resolving and correctly displaying the evolution of the major variants of concern. Using these numerical datasets, through a pairwise comparison of sets of proteolytic peptide masses for each protein, the tree is built without the need for the sequence data itself or any sequence alignment. In the same analysis, single point mutations are calculated from peptide mass differences of different protein sets and these are displayed at the branch nodes on the tree. The tree topology is found to be consistent with that generated using conventional sequence-based phylogenetics by a manual visualisation and using a tree comparison algorithm. The mass tree resolves major variants of the virus and displays non-synonymous mutations, calculated based on the mass data alone, on the tree that enable protein evolution to be charted and tracked along interconnected branches. Tracking the evolution of the SARS-CoV2 coronavirus S-protein is of particular importance given its role in the attachment of the virus to host cells ahead of viral replication.

Study of Melipona quadrifasciata brain under operant learning using proteomic and phosphoproteomic analysis.

Learning to anticipate events based on the predictive relationship between an action and an outcome (operant conditioning) is a form of associative learning shared by humans and most of other living beings, including invertebrates. Several behavioral studies on the mechanisms of operant conditioning have included Melipona quadrifasciata, a honey bee that is easily manipulated due to lack of sting. In this work, brain proteomes of Melipona bees trained using operant conditioning and untrained (control) bees were compared by two-dimensional gel electrophoresis analysis within pI range of 3-10 and 4-7; in order to find proteins specifically related to this type of associative learning.One protein was detected with differential protein abundance in the brains of trained bees, when compared to not trained ones, through computational gel imaging and statistical analysis. This protein was identified by peptide mass fingerprinting and MS/MS peptide fragmentation using a MALDI-TOF/TOF mass spectrometer as one isoform of arginine kinase monomer, apparently dephosphorylated. Brain protein maps were obtained by 2-DE (Two-dimensional gel electrophoresis) from a total proteins and phosphoproteins extract of the bee Melipona quadrifasciata. One isoform of arginine kinase, probably a dephosphorylated isoform, was significantly more abundant in the brain of trained bees using operant conditioning. Arginine kinase has been reported as an important enzyme of the energy releasing process in the visual system of the bee, but it may carry out additional and unexpected functions in the bee brain for learning process.

Metabolite profiling from different parts of tender fruit endosperm of Borassus flabellifer L. (ice apple).

Borassus flabellifer L., commonly known as Asian palmyra, is native to South and Southeast Asia. The endosperms of B. flabellifer (known as nungu in Dravidian culture) are widely consumed during the summer season. It is rich in various nutrients and helps in reducing weight, treating skin and digestive issues, lowering body temperature, and managing migraines and diabetes. This study focuses on identifying the small molecules and proteins from the two varieties of B. flabellifer tender fruit endosperms collected from districts around Chennai, Tamil Nadu, India. The collected free nuclear endosperm was subjected to direct extraction and the mesocarp and cellular endosperms were lyophilized and homogenized. Metabolites were extracted by hexane, methanol, and chloroform and investigated using gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). The compounds identified were from the classes of carboxylic acids, flavonoids, amino acids, alkaloids, fatty acids, oligopeptides, vitamins, and glycosides. High-performance liquid chromatography (HPLC) technique was employed to estimate the quantity of amino acids, wherein the total amino acid in the green variety was found to be higher than in the black variety. Proteins were identified after simulating with a gastrointestinal enzyme using liquid chromatography tandem mass spectrometry (LC-MS/MS)-based peptide mass fingerprinting. The different mineral oxides present in the tender fruit endosperm were identified using X-ray diffraction studies, which confirmed the presence of mineral oxides, such as Br1.25ClO2.75Pb3.88, calcium zirconium tantalum oxide, and barium fluoroniobate. This study validates the presence of bioactive metabolites in green and black varieties of B. flabellifer tender fruit endosperm with a range of activities, such as anti-inflammatory, antibacterial, anticancer, and anti-diabetic properties.

Measurement of kinetic isotope effects on peptide hydroxylation using MALDI-MS.

Primary kinetic isotope effects (KIEs) provide unique insight into enzymatic reactions, as they can reveal rate-limiting steps and detailed chemical mechanisms. HIF hydroxylases, part of a family of 2-oxoglutarate (2OG) oxygenases are central to the regulation of many crucial biological processes through O2-sensing, but present a challenge to monitor due to the large size of the protein substrate and the similarity between native and hydroxylated substrate. MALDI-TOF MS is a convenient tool to measure peptide masses, which can also be used to measure the discontinuous kinetics of peptide hydroxylation for Factor Inhibiting HIF (FIH). Using this technique, rate data can be observed from the mole-fraction of CTAD and CTAD-OH in small volumes, allowing noncompetitive H/D KIEs to be measured. Slow dCTAD substrate leads to extensive uncoupling of O2 consumption from peptide hydroxylation, leading to enzyme autohydroxylation, which is observed using UV-vis spectroscopy. Simultaneously measuring both the normal product, CTAD-OH, and the uncoupled product, autohydroxylated enzyme, the KIE on the microscopic step of hydrogen atom transfer (HAT) can be estimated. MALDI-MS analysis is a strong method for monitoring reactions that hydroxylate peptides, and can be generalized to other similar reactions, and simultaneous kinetic detection of branched products can provide valuable insight on microscopic KIEs at intermediate mechanistic steps.

Salivary Peptide Profiling Analysis of Patients with Periodontitis and Chronic Obstructive Pulmonary Disease

To analyze the salivary peptide profiles of patients with periodontitis (PD) and chronic obstructive pulmonary disease (COPD), to identify differentially expressed peptides that are associated with diseases, to explore for biomarkers with potential diagnostic significance, and to probe for new perspectives for the early prevention and treatment of COPD. A total of 10 PD patients (the PD group), 10 PD patients with COPD (the PD plus COPD group), and 8 healthy controls (the Control group) were selected for the study. The clinical data and saliva samples of the subjects were collected. Salivary supernatant samples were separated and purified with weak-cation-exchange magnetic bead-based (WCX-MB). With matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), the biodata of the samples were obtained and differential salivary peptide profiling was conducted to screen for peptides exhibiting inter-group differences. In addition, all the differentially expressed peptides were examined and verified with liquid chromatography tandem mass spectrometry (LC-MS/MS). An average of 77 peptide mass peaks were detected among three groups, the peaks intensities differed significantly for 10 peptides between PD patients and PD patients with COPD. Among them, eight peptides (1193.5, 1836.2, 1735.1, 1321.3, 1356.8, 2086.8, 1863.6, and 2230.9) showed increased expression and two peptides (1067.3 and 1124.4) showed decreased expression in the PD plus COPD group, in comparison with the PD group. Among the 10 differential peptides, 1193.5 and 1356.8 were identified as histidine-rich protein-1, submaxillary gland androgen-regulated protein 3B, and salivary acidic proline-rich protein 1/2. With WCX-MB and MALDI-TOF-MS, we have identified, from the saliva of patients with concomitant PD and COPD, differentially expressed salivary peptides that were associated with diseases. The differentially expressed peptides thus screened out show promises for being used as auxiliary biomarkers for early diagnosis of COPD.

Proteolytic Activity against the Distal Polybasic Tract of the Gamma Subunit of the Epithelial Sodium Channel ENaC in Nephrotic Urine.

Experimental nephrotic syndrome in mice leads to proteolytic activation of the epithelial sodium channel ENaC, possibly involving the distal polybasic tract of its γ-subunit (183RKRK). We sought to determine if urine samples from both nephrotic mice and a cohort of patients with acute nephrotic syndrome contain a specific proteolytic activity against this region of γ-ENaC. A peptide substrate consisting of amino acids 180-194 of murine γ-ENaC was N-terminally coupled to a fluorophore, yielding AMCA-FTGRKRKISGKIIHK. The substrate was incubated with nephrotic urine samples from mice as well as patients with or without the serine protease inhibitor, aprotinin. The digested peptides were separated on a reverse phase HPLC and detected with a fluorescence detector (350/450 nm). Peptide masses of the peaks were determined with a MALDI-TOF mass spectrometer. In addition, urinary proteolytic activity was quantitated using AMC-coupled substrates reflecting different cleavage sites within the polybasic tract. No significant proteolytic activity against the substrate was found in the urine of healthy humans or mice. Incubation with urine samples of nephrotic patients (n = 8) or mice subjected to three different models of experimental nephrotic syndrome (n = 4 each) led to cleavage of the substrate within the polybasic tract prevented by the serine protease inhibitor aprotinin. The most dominant cleavage product was FTGRKR in both species, which was confirmed using quantitative measurements with FTGRKR- AMC. Nephrotic urine from both humans and mice contains aprotinin-sensitive proteolytic activity against the distal polybasic tract of γ-ENaC, reflecting excretion of active proteases in the urine or proteasuria.

Species identification of early colonial bone artefacts excavated from Pyrmont, Australia, by mass spectrometric identification of collagen peptides

Zooarchaeology by Mass Spectrometry (ZooMS) is a peptide mass fingerprinting technique that analyses Collagen 1A1 and 1A2 marker peptides for the genus- or species-level identification of fragmentary bones in the archaeological record. Traditionally, this analysis is performed using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-ToF-MS) to identify characteristic m/z values of known marker peptides. Here we present data on the application of a modified paleoproteomics approach, using nanoflow liquid chromatography - tandem mass spectrometry proteomics, to the analysis of a collection of six early colonial Australian (early to mid-19th Century CE) worked bone artefacts, believed to be mostly knife handles, excavated from a site in Pyrmont, Sydney, Australia in 2017. We were successfully able to identify characteristic marker peptides for bovine COL1A1 and COL1A2 in all six bone artefacts.

A comparison of minimally-invasive sampling techniques for ZooMS analysis of bone artifacts

Bone and antler are important raw materials for tool manufacture in many cultures, past and present. The modification of osseous features which take place during artifact manufacture frequently make it difficult to identify either the bone element or the host animal, which can limit our understanding of the cultural, economic, and/or symbolic factors which influence raw material acquisition and use. While biomolecular approaches can provide taxonomic identifications of bone or antler artifacts, these methods are frequently destructive, raising concerns about invasive sampling of culturally-important artifacts or belongings. Collagen peptide mass fingerprinting (Zooarchaeology by Mass Spectrometry or ZooMS) can provide robust taxonomic identifications of bone and antler artifacts. While the ZooMS method commonly involves destructive subsampling, multiple minimally-invasive sampling techniques also exist. In this paper, we compare three previously proposed minimally-invasive sampling methods (forced bag, eraser, and polishing film) on an assemblage of 15 bone artifacts from the pre-contact site EjTa-4, a large midden complex located on Calvert Island, British Columbia, Canada. We compare the results of the minimally-invasive methods to 10 fragmentary remains sampled using the conventional destructive ZooMS method. We assess the reliability and effectiveness of these methods by comparing MALDI-TOF spectral quality, the number of diagnostic and high molecular weight peaks as well as the taxonomic resolution reached after identification. We find that coarse fiber-optic polishing films are the most effective of the minimally-invasive techniques compared in this study, and that the spectral quality produced by this minimally-invasive method was not significantly different from the conventional destructive method. Our results suggest that this minimally-invasive sampling technique for ZooMS can be successfully applied to culturally significant artifacts, providing comparable taxonomic identifications to the conventional, destructive ZooMS method.

Your horse is a donkey! Identifying domesticated equids from Western Iberia using collagen fingerprinting

Skeletal remains of two equid species, Equus caballus (horse) and Equus asinus (donkey), have been found in archaeological contexts throughout Iberia since the Palaeolithic and Chalcolithic periods, respectively. These two species play different economic and cultural roles, and therefore it is important to be able to distinguish between the two species to better understand their relative importance in the past human societies. The most reliable morphological features for distinguishing between the two domesticated equids are based on cranial measurements and tooth enamel folds, leading to only a small percentage of archaeological remains that can be identified to species. Ancient DNA (aDNA) analysis can be used to reliably distinguish the two equids, but it can be cost prohibitive to apply to large assemblages, and aDNA preservation of non-cranial elements is often low. Collagen peptide mass fingerprinting by matrix-assisted laser desorption time-of-flight (MALDI-TOF) mass spectrometry, also known as zooarchaeology by mass spectrometry (ZooMS), is a minimally destructive and cost-effective alternative to aDNA analysis for taxonomic determination. However, current ZooMS markers lack resolution below the genus level Equus. In this paper, we report a novel ZooMS peptide marker that reliably distinguishes between horses and donkeys using the enzyme chymotrypsin. We apply this peptide marker to taxonomically identify bones from the Iberian Peninsula ranging from the Iron Age to the Late Modern Period. The peptide biomarker has the potential to facilitate the collection of morphological data for zooarchaeological studies of equids in Iberia and throughout Eurasia and Africa.

Proteomic Characterisation of the Plasma Proteome in Extramedullary Multiple Myeloma Identifies Potential Prognostic Biomarkers

Introduction: Extramedullary multiple myeloma (EMM) is an aggressive manifestation of multiple myeloma (MM) reported to occur in approximately 7% of patients at diagnosis and up to 30% of patients at relapse. EMM is characterised by the spread of malignant plasma cells from the bone marrow microenvironment to distal tissues or organs. It is associated with an adverse prognosis, correlating with a significant reduction in overall survival. Currently there are no validated, established biomarkers to predict EMM. Furthermore, EMM is often treated similarly to high-risk MM with no targeted therapeutic strategies. In-depth proteomic studies on EMM are lacking and the underlying molecular mechanisms that facilitate extramedullary transition are yet to be fully defined. Novel biomarkers and therapeutic targets are urgently required. To enhance our understanding of EMM and to identify novel prognostic biomarkers, we performed a mass spectrometry-based proteomic study on plasma from MM patients with and without extramedullary spread. Methods: Label-free liquid chromatography mass spectrometric analysis of age and gender-matched medullary MM (n=8) and EMM (n=9) blood plasma samples was carried out using a Thermo Q-Exactive mass spectrometer (Thermo Fisher Scientific). Proteome Discoverer 2.2 using Sequest HT (Thermo Fisher Scientific) and a percolator were employed for the identification of peptides and proteins. Several parameters were defined for protein identification: MS/MS mass tolerance was set to 0.02 Da; peptide mass tolerance was set to 10ppm; methionine oxidation was set as a variable modification; carbamido-methylation was set as a fixed modification; and up to two missed cleavages were tolerated. Peptide probability was set to high confidence. Data was imported into Perseus (1.6.14.0) for further analysis. Proteins with less than 70% valid values were removed from the analysis. Proteins of interest were identified based on an FDR-adjusted p-value ≤0.1, fold change >1.5 between experimental groups. Six proteins were selected for further validation using DuoSet enzyme linked immunosorbent assay (ELISA) kits (R&D Systems). We performed receiver operating characteristic (ROC) and area under the curve (AUC) analyses to determine the diagnostic potential of the validated proteins. Results: The median age was 65. Survival analysis revealed a statistically significant change in overall survival (OS) between the two patient cohorts (Log-rank = 3.977, P = 0.046). The median OS of patients with EMM and those without extramedullary spread was 19 months and 83 months, respectively. Our quantitative MS-based proteomic analysis identified 21 proteins of differential abundance between EMM and MM patient plasma (False discovery rate (FDR)-adjusted p-value < 0.1, fold change > 1.5) (Fig. 1A). Antibody-based validation using ELISAs was performed on six proteins (vascular cell adhesion molecule 1 (VCAM1), hepatocyte growth factor activator (HGFA), pigment epithelial-derived factor (PEDF), alpha-2-macroglobulin (A2M), cholinesterase (BCHE), aminopeptidase N (CD13)). VCAM1, HGFA and PEDF were confirmed as being significantly altered between the two cohorts (FDR-adjusted p-value < 0.05). VCAM1, HGFA and PEDF were subject to ROC analyses, demonstrating high discriminatory power for EMM diagnosis (AUC = 0.96, AUC = 0.85, and AUC = 0.97, respectively). The diagnostic efficacy was further enhanced by combining these biomarkers using a logistic regression model (AUC = 1). Conclusion: Our mass spectrometry and antibody-based study identified proteins of differential abundance in the blood plasma of MM patients with and without extramedullary spread. VCAM1, PEDF and HGFA represent promising predictive biomarkers and warrant further investigation in a larger cohort of patients. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

The AtoC family response regulator upregulates an operon encoding putative outer membrane proteins sorted by type IX secretion system in Porphyromonas gingivalis

ObjectivesPorphyromonas gingivalis, a keystone periodontopathogen, has multiple two-component systems that are thought to modulate virulence. In this study, we focused on PGN_0775 response regulator (RR), an AtoC homolog, and attempted to identify the target gene that it regulates in P. gingivalis. MethodsComparative proteomic analyses comprising two-dimensional electrophoresis and peptide mass fingerprinting were applied to total protein samples from parent (WT) and atoC gene knockout (KO) strains to screen for affected protein spots. Fluctuations in the expression of corresponding genes were further confirmed using relative quantitative real-time polymerase chain reaction (RQPCR). ResultsFive protein spots with fluctuating expression levels were identified in pgn_0775 KO strains along with their masses and physiological features, which contained two hypothetical proteins with higher expression levels in the WT than in the KO strains. RQPCR analysis confirmed that mRNA levels were consistently decreased in KO and recovered in pgn_0775-complemented KO strains. The two hypothetical proteins appeared to be the products of an operon that comprises four genes encoding three hypothetical but putative type IX secretion system sorting domain-containing proteins and an N-terminal region of the C25 cysteine peptidase. ConclusionsThe AtoC RR homolog in P. gingivalis upregulates the expression of the operon encoding potentially antigenic proteins retained on the cell surface; thus, it could be a promising target for P. gingivalis-specific antivirulence therapy.

Surface Decoration of Peptide Nanoparticles Enables Efficient Therapy toward Osteoporosis and Diabetes

AbstractA versatile surface decoration strategy to efficiently encapsulate water‐soluble peptides is developed. By assembling peptide molecules into nanoparticles, diverse physiochemical properties of these compacted molecules are equalized to the surface properties of nanoparticles. Primarily driven by the generic electrostatic attractions, the surface of as‐prepared peptide nanoparticles is decorated with charged amino acids‐grafted poly(lactic‐co‐glycolic acid). This adsorbed polymer layer versatilely blocks the phase transfer of peptide nanoparticles by increasing their affinity to the dispersed phase solvent molecules. Attributed to the ultrahigh encapsulation efficiencies (&gt; 96%), the peptide mass fraction inside the obtained microcomposites is higher than 48%. The plasma calcium level has been efficiently reduced for ≈3 weeks with only one single injection of salmon calcitonin‐encapsulated microcomposite in osteoporotic rats. Similarly, one single injection of exenatide‐encapsulated microcomposites efficiently controls the glycemic level in type 2 diabetic rats for up to 3 weeks. Overall, the developed versatile surface decoration strategy efficiently encapsulates peptides and improves their pharmacokinetic features, regardless of the molecular structure of peptide cargos.

111In]In-CP04 as a novel cholecystokinin-2 receptor ligand with theranostic potential in patients with progressive or metastatic medullary thyroid cancer: final results of a GRAN-T-MTC Phase I clinical trial

IntroductionMedullary thyroid cancer (MTC) is a rare malignant tumour of the parafollicular C-cells with an unpredictable clinical course and currently suboptimal diagnostic and therapeutic options, in particular in advanced disease. Overexpression of cholecystokinin-2 receptors (CCK2R) represents a promising avenue to diagnostic imaging and targeted therapy, ideally through a theranostic approach.Materials and methodsA translational study (GRAN-T-MTC) conducted through a Phase I multicentre clinical trial of the indium-111 labelled CP04 ([111In]In-CP04), a CCK2R-seeking ligand was initiated with the goal of developing a theranostic compound. Patients with proven advanced/metastatic MTC or short calcitonin doubling time were enrolled. A two-step concept was developed through the use of low- and high-peptide mass (10 and 50 μg, respectively) for safety assessment, with the higher peptide mass considered appropriate for therapeutic application. Gelofusine was co-infused in a randomized fashion in the second step for the evaluation of potential reduction of the absorbed dose to the kidneys. Imaging for the purpose of biodistribution, dosimetry evaluation, and diagnostic assessment were performed as well as pre-, peri-, and postprocedural clinical and biochemical assessment.ResultsSixteen patients were enrolled. No serious adverse events after application of the compound at both peptide amounts were witnessed; transient tachycardia and flushing were observed in two patients. No changes in biochemistry and clinical status were observed on follow-up. Preliminary dosimetry assessment revealed the highest dose to urinary bladder, followed by the kidneys and stomach wall. The effective dose for 200 MBq of [111In]In-CP04 was estimated at 7±3 mSv and 7±1 mSv for 10 μg and 50 μg CP04, respectively. Administration of Gelofusine reduced the dose to the kidneys by 53%, resulting in the organ absorbed dose of 0.044±0.019 mSv/MBq. Projected absorbed dose to the kidneys with the use of [177Lu]Lu-CP04 was estimated at 0.9±0.4 Gy/7.4 GBq. [111In]In-CP04 scintigraphy was positive in 13 patients (detection rate of 81%) with superior diagnostic performance over conventional imaging.ConclusionIn the present study, [111In]In-CP04 was shown to be a safe and effective radiopharmaceutical with promising theranostic characteristics for patients with advanced MTC.

Carboxyl Terminus of HOATZ is Intrinsically Disordered and Interacts with Heat Shock Protein A Families.

Hoatz is a vertebrate-specific gene, the defects of which result in hydrocephalus and oligo-astheno-teratozoospermia in mice. It encodes a 19-kDa protein lacking any domains of known function. To understand the protein activity, we purified the carboxyl-terminal fragment that is conserved among different species, and analyzed its structure and potential binding proteins. A soluble 9.9-kDa HOATZ fragment, including a poly-histidine tag (designated HOATZ-C), was purified to homogeneity. The gel filtration profile and circular dichroism spectra collectively indicated that HOATZ-C was intrinsically disordered. When HOATZ-C was mixed with cleared lysate from Hoatz-null mouse testis, several proteins, including two of ~70 kDa size, were specifically co-purified with HOATZ-C on a nickel column. Based on the peptide mass fingerprinting of these bands, two members of the heat-shock protein family A were identified. These data may indicate the role of HOATZ in stress regulation in cells characterized by motile cilia and flagella.

Structural and Functional Analysis of Peptides Derived from KEX2-Processed Repeat Proteins in Agaricomycetes Using Reverse Genetics and Peptidomics.

Bioactivities of fungal peptides are of interest for basic research and therapeutic drug development. Some of these peptides are derived from "KEX2-processed repeat proteins" (KEPs), a recently defined class of precursor proteins that contain multiple peptide cores flanked by KEX2 protease cleavage sites. Genome mining has revealed that KEPs are widespread in the fungal kingdom. Their functions are largely unknown. Here, we present the first in-depth structural and functional analysis of KEPs in a basidiomycete. We bioinformatically identified KEP-encoding genes in the genome of the model agaricomycete Coprinopsis cinerea and established a detection protocol for the derived peptides by overexpressing the C. cinerea KEPs in the yeast Pichia pastoris. Using this protocol, which includes peptide extraction and mass spectrometry with data analysis using the search engine Mascot, we confirmed the presence of several KEP-derived peptides in C. cinerea, as well as in the edible mushrooms Lentinula edodes, Pleurotus ostreatus, and Pleurotus eryngii. While CRISPR-mediated knockout of C. cinerea kep genes did not result in any detectable phenotype, knockout of kex genes caused defects in mycelial growth and fruiting body formation. These results suggest that KEP-derived peptides may play a role in the interaction of C. cinerea with the biotic environment and that the KEP-processing KEX proteases target a variety of substrates in agaricomycetes, including some important for mycelial growth and differentiation. IMPORTANCE Two recent bioinformatics studies have demonstrated that KEX2-processed repeat proteins are widespread in the fungal kingdom. However, despite the prevalence of KEPs in fungal genomes, only few KEP-derived peptides have been detected and studied so far. Here, we present a protocol for the extraction and structural characterization of KEP-derived peptides from fungal culture supernatants and tissues. The protocol was successfully used to detect several linear and minimally modified KEP-derived peptides in the agaricomycetes C. cinerea, L. edodes, P. ostreatus, and P. eryngii. Our study establishes a new protocol for the targeted search of KEP-derived peptides in fungi, which will hopefully lead to the discovery of more of these interesting fungal peptides and allow a further characterization of KEPs.

Laboratory Diagnostic Methods and Antibiotic Resistance Patterns of Staphylococcus aureus and Escherichia coli Strains: An Evolving Human Health Challenge.

Raw ground meat is known as a transmission vehicle for biological agents that may be harmful to human health. The objective of the present study was to assess microbiological quality of the ground meats. A total of 280 samples of local and imported chilled meats were randomly collected from retail shops in Buraydah City, Saudi Arabia. The meat samples were microbiologically analyzed using standard methods, peptide mass fingerprinting (PMF) technique, MicroScan Walkaway System (MicroScan) and qPCR System. The imported meat was more bacterially contaminated than local meat, with variable contamination degrees of Staphylococcus aureus (40.33%), Escherichia coli (36.13%), Hafnia alvei (7.56%), Pseudomonas spp. (6.72%), Salmonella spp. (5.88%) and Aeromonas spp. (3.36%). PMF verified all the isolated bacteria by 100%, compared to 75-95% achieved by MicroScan. The gene encoding flagellin (fliC) was recognized in 67.44% of E. coli strains, while the thermonuclease (nuc) and methicillin resistance (mecA) genes were detected in 100% S. aureus and 39.6% of methicillin-resistant S. aureus (MRSA) strains, respectively. The S. aureus and E. coli strains were highly resistant to multiple antibiotics (e.g., ampicillin, amoxicillin-clavulanic acid and cephalothin). For identifying various foodborne pathogens, PMF has been recognized as a powerful and precise analytical method. In light of the increasing use of PMF to detect multidrug-resistant bacteria, this study emphasizes the need for improved ways of treating and preventing pathogens, as well as setting up monitoring systems to guarantee hygiene and safety in meat production.

Nonspecific phospholipase C3 of radish has phospholipase D activity towards glycosylinositol phosphoceramide.

Glycosylinositol phosphoceramide (GIPC) is a major sphingolipid in the plasma membranes of plants. Previously, we found an enzyme activity that produces phytoceramide 1-phosphate (PC1P) by hydrolysis of the D position of GIPC in cabbage and named this activity as GIPC-phospholipase D (PLD). Here, we purified GIPC-PLD by sequential chromatography from radish roots. Peptide mass fingerprinting analysis revealed that the potential candidate for GIPC-PLD protein was nonspecific phospholipase C3 (NPC3), which has not been characterized as a PLD. The recombinant NPC3 protein obtained by heterologous expression system in Escherichia coli produced PC1P from GIPC and showed essentially the same enzymatic properties as those we characterized as GIPC-PLD in cabbage, radish and Arabidopsis thaliana. From these results, we conclude that NPC3 is one of the enzymes that degrade GIPC.

In vitro immunomodulatory and antioxidant effects of oligopeptides and four characteristic peptides in black-bone silky fowl (Gallus gallus domesticus Brisson).

Black-bone silky fowl (Gallus gallus domesticus Brisson) is considered to have strengthening effect on the body and immunomodulatory effects. The black-bone silky fowl peptide (BSFP) was produced by enzymatic digestion of the whole black-bone silky fowl (including the head and claws) after removal of the viscera. Afterwards, the four of the characteristic peptides Glu-Phe (EF), Glu-Glu-Leu (EEL), Glu-His-Pro-Thr (EHPT), Ala-Gly-Gly-His (AGGF) of the BSFP were identified by HPLC-MS/MS. The preventive effects of BSFP and the four characteristic peptides on antioxidant and immunomodulation were investigated. The antioxidant capacity was assessed by in vitro HepG2 intracellular reactive oxygen species (ROS). The immunomodulatory experiments were conducted by measuring the effects of the BSFP and four peptides on the proliferation of splenocytes, T and B lymphocytes cells, the CD4+ /CD8+ T lymphocytes ratio, and the phagocytic capacity of macrophages and the nitric oxide (NO) content of macrophages. The four peptides of BSFP showed strong antioxidant capacity, with the most potent peptide for intracellular ROS being AGGF, with 56% inhibition. AGGF, EF, and BSFP showed highly positive effects on splenocyte proliferation and when Concanavalin A (ConA) was used as a stimulus for T lymphocytes and lipopolysaccharide (LPS) as a stimulus for B lymphocytes, the peptides stimulated cell proliferation in a dose-dependent manner. Of these, EF, AGGF, and BSFP promoted the proliferation of T lymphocytes; EF, EHPT, and BSFP significantly promoted the proliferation of B lymphocytes. EHPT and BSFP increased the CD4+ /CD8+ ratio of T cells. Needle aspiration of neutral red was significantly promoted by macrophages treated with peptides other than EF. In addition, EEL, EHPT, AGGF, and BSFP had a promotive effect on NO production in phagocytes. The results indicate that BSFP is a peptide product with good immunomodulatory functions, four peptides identified from BSFP show outstanding effects in terms of antioxidant properties and immunomodulation. PRACTICAL APPLICATIONS: In this study, the amino acid composition and relative molecular masses of the black-bone silky fowl peptide were analyzed, while the four peptides with significant effects on antioxidant and immunomodulatory properties in black-bone silky fowl peptide were identified by HPLC-MS/MS technique. Positive effects of black-bone silky fowl peptide and its four peptides on antioxidant capacity and immunomodulatory ability as revealed by cell experiments. The results of this experiment provide a preliminary theoretical basis for the development of new functional foods using black-bone silky fowl peptide and their characteristic peptides.