Mass Spectrometry Analysis Of Proteins Research Articles

Unbiased plasma profiling using pre-selected RNA aptamer pools predicts mortality in COVID-19 and identifies protein risk factors

The impact of the COVID-19 pandemic demands effective prognostic tools for precise risk evaluation and timely intervention. This study utilised the APTASHAPE technology to profile plasma proteins in COVID-19 patient samples. Employing a highly diverse 2’-fluoro-protected RNA aptamer pool enriched toward proteins in the plasma samples from COVID-19 patients, we performed a single round of parallel selection on the derivation cohort and identified 93 discriminatory aptamers capable of distinguishing COVID-19 and healthy plasma samples. A subset of these aptamers were then used to predict 30-day mortality with high sensitivity and specificity in a validation cohort of 165 patients. We predicted 30-day mortality with an Area Under Curve (AUC) of 0.91 in females and 0.68 in males. Affinity purification coupled with mass spectrometry analysis of the aptamer-targeted proteins identified potential biomarkers associated with disease severity, including complement system components. The study demonstrates the APTASHAPE technology as an unbiased approach that not only aids in predicting disease outcomes but also offers insights into gender-specific differences, shedding light on the nuanced aspects of COVID-19 pathophysiology. In conclusion, the findings highlight the promise of APTASHAPE as a valuable tool for estimating risk factors in COVID-19 patients and enabling stratification for personalised treatment management.

Ultrasensitive Proteomics of Trace Cardiac Tissues with Anchor-Nanoparticles.

Pathological cardiac hypertrophy is a complex process that often leads to heart failure. Label-free proteomics has emerged as an important platform to reveal protein variations and to elucidate the mechanisms of cardiac hypertrophy. Endomyocardial biopsy is a minimally invasive technique for sampling cardiac tissue, but it yields only limited amounts of an ethically permissible specimen. After regular pathological examination, the remaining trace samples pose significant challenges for effective protein extraction and mass spectrometry analysis. Herein, we developed trace cardiac tissue proteomics based on the anchor-nanoparticles (TCPA) method. We identified an average of 6666 protein groups using ∼50 μg of myocardial interventricular septum samples by TCPA. We then applied TCPA to acquire proteomics from patients' cardiac samples both diagnosed as hypertrophic hearts and myocarditis controls and identified significant alterations in pathways such as regulation of actin cytoskeleton, oxidative phosphorylation, and cGMP-PKG signaling pathway. Moreover, we found multiple lipid metabolic pathways to be dysregulated in transthyretin cardiac amyloidosis compared to other types of cardiac hypertrophy. TCPA offers a new technique for studying pathological cardiac hypertrophy and can serve as a platform toolbox for proteomic research in other cardiac diseases.

Quantitative profiling of cochlear synaptosomal proteins in cisplatin-induced synaptic dysfunction

The disruption of ribbon synapses in the cochlea impairs the transmission of auditory signals from the cochlear sensory receptor cells to the auditory cortex. Although cisplatin-induced loss of ribbon synapses is well-documented, and studies have reported nitration of cochlear proteins after cisplatin treatment, yet the underlying mechanism of cochlear synaptopathy is not fully understood. This study tests the hypothesis that cisplatin treatment alters the abundance of cochlear synaptosomal proteins, and selective targeting of nitrative stress prevents the associated synaptic dysfunction. Auditory brainstem responses of mice treated with cisplatin showed a reduction in amplitude and an increase in latency of wave I, indicating cisplatin-induced synaptic dysfunction. The mass spectrometry analysis of cochlear synaptosomal proteins identified 102 proteins that decreased in abundance and 249 that increased in abundance after cisplatin treatment. Pathway analysis suggested that the dysregulated proteins were involved in calcium binding, calcium ion regulation, synapses, and endocytosis pathways. Inhibition of nitrative stress by co-treatment with MnTBAP, a peroxynitrite scavenger, attenuated cisplatin-induced changes in the abundance of 27 proteins. Furthermore, MnTBAP co-treatment prevented the cisplatin-induced decrease in the amplitude and increase in the latency of wave I. Together, these findings suggest a potential role of oxidative/nitrative stress in cisplatin-induced cochlear synaptic dysfunction.

208 Preliminary Results of Novel Method for Identifying Ischemic Stroke Vesicular Protein Signature in Cardiac Surgery Patients

INTRODUCTION: Acute ischemic stroke (AIS) treatment depends on timely diagnosis. Identifying an efficient, blood-based protein signature for AIS has been limited by the lack of a pre-ischemia control group. Here we report the preliminary results of a model for AIS protein signature discovery using cardiac surgery patients and novel mass spectrometry techniques. METHODS: Twenty patients undergoing aortic arch repair with deep hypothermic circulatory arrest (n = 17) or coronary artery bypass graft (n = 3) were enrolled. Blood samples were obtained immediately pre- and postoperatively. Magnetic resonance imaging (MRI) of the brain was obtained within 72 hours of surgery. Presence of infarct and total ischemic volume was determined. A novel protein enrichment and mass spectrometry analysis technique (MAG-Net) was used to characterize the pre- and post-surgical proteomes present in extracellular vesicles. Analysis of variance (ANOVA) (false discovery rate < 0.05) was used to analyze protein signatures associated with infarction. RESULTS: Post-surgical infarct occurred in 15 patients (75%), with a median volume of 108mm3. A total of 5,376 proteins were identified, 1,125 of which showed a significant difference between paired pre- and post-operative concentrations. Of these 1,125 proteins, 524 proteins were unique to patients without infarction, 340 proteins had a significant change in both populations, and 261 proteins were unique to patients with infarcts. There were no significant proteins for the interaction term comparing pre- and post-operative differences between the infarct/no infarct groups. CONCLUSIONS: This clinical model for AIS protein signature development relies on the high rate of ischemia during cardiac surgery to allow for pre-stroke sample collection. The MAG-Net technique enables efficient processing of biologically relevant extracellular vesicle proteins and analysis of an unbiased protein signature. The preliminary results demonstrate the feasibility of combining these innovations for AIS protein signature discovery.

Mechanism of oxalate decarboxylase Oxd_S12 from Bacillus velezensis BvZ45-1 in defense against cotton verticillium wilt.

Verticillium wilt, a soilborne vascular disease caused by Verticillium dahliae, strongly affects cotton yield and quality. In this study, an isolated rhizosphere bacterium, designated Bacillus velezensis BvZ45-1, exhibited greater than 46% biocontrol efficacy against cotton verticillium wilt under greenhouse and field conditions. Moreover, through crude protein extraction and mass spectrometry analysis, we found many antifungal compounds present in the crude protein extract of BvZ45-1. The purified oxalate decarboxylase Odx_S12 from BvZ45-1 inhibited the growth of V. dahliae Vd080 by reducing the spore yield, causing mycelia to rupture, and causing spore morphology changes, cell membrane rupture and cell death. Subsequently, overexpression of Odx_S12 in Arabidopsis significantly improved plant resistance to V. dahliae. Through studies of the resistance mechanism of Odx_S12, V. dahliae was shown to produce oxalic acid (OA), which has a toxic effect on Arabidopsis leaves. Odx_S12 overexpression reduced Arabidopsis OA content, enhanced tolerance to OA, and improved resistance to verticillium wilt. Transcriptome analysis and quantitative real-time PCR (qRT-PCR) analysis revealed that Odx_S12 promoted the outbreak of reactive oxygen species (ROS) and a salicylic acid (SA) and abscisic acid (ABA) mediated defense response in Arabidopsis. In summary, this study not only identified B. velezensis BvZ45-1 as an efficient biological control agent, but also identified the resistance gene Odx_S12 as a candidate for cotton breeding against verticillium wilt.

Fibulin-1 promotes intimal hyperplasia after venous stent implantation through ACE mediated angiotensin II signaling

ObjectiveStent intimal hyperplasia leads to in stent restenosis and thrombosis. This study determined whether Fibulin-1 activity in smooth muscle cells (SMCs) contributes to stent restenosis or thrombosis. MethodsStent implantation was conducted in a pig model. Target vessel samples were stained and analyzed by protein mass spectrometry. Cell experiments and Fibulin-1 SMC specific knockout mice (Fbln1SMKO) were used to investigate the mechanism of Fibulin-1 induced SMC proliferation and thrombosis. ResultsSMC proliferation and phenotypic transition are the main pathological changes of intimal hyperplasia in venous stents. Protein mass spectrometry analysis revealed a total of 67 upregulated proteins and 39 downregulated proteins in intimal hyperplasia after stent implantation compared with normal iliac vein tissues. Among them, Fibulin-1 ranked among the top proteins altered. Fibulin-1 overexpressing human SMCs (Fibulin-1-hSMCs) showed increased migration and phenotypic switching from contractile to secretory type and Fibulin-1 inhibition decreased the activity of SMCs. Mechanistically, Fibulin-1-hSMCs displayed increased levels of angiotensin converting enzyme (ACE) expression and angiotensin II signaling. Inhibition of ACE or angiotensin II signaling alleviated the migration of Fibulin-1-hSMCs. Using Fibulin-1 SMC specific knockout mice (Fbln1SMKO) and venous thrombosis model, we demonstrated that Fibulin-1 deletion attenuated intimal SMCs proliferation and thrombosis. Further, Fibulin-1 concentration was high in iliac vein compression syndrome (IVCS) patients treated with stent and was an independent predictor of venous insufficiency. ConclusionsFibulin-1 promotes SMC proliferation partially through ACE secretion and angiotensin II signaling after stent implantation. Fibulin-1 plays a role in venous insufficiency syndrome, implicating the protein in the detection and treatment of IVCS.

Lipoxygenase LOX3 Is the Enigmatic Tocopherol Oxidase in Runner Bean (Phaseolus coccineus).

Purification of extracts from the etiolated seedlings of runner bean (Phaseolus coccineus), coupled with mass spectrometry analysis of proteins revealed that the enzyme responsible for tocopherol oxidation activity is lipoxygenase, an enzyme known for enzymatic lipid peroxidation of unsaturated lipids. Biochemical analysis of the activity, along with the expression profile of three LOX isoforms (LOX1, LOX2, LOX3) in various parts of the etiolated seedlings, revealed that LOX3 was the major isoform expressed in the epicotyls, indicating that this isoform was responsible for the tocopherol oxidation activity; in the primary leaves, besides LOX3, the other two isoforms might have also contributed to the activity. The experiments performed in the model systems showed that unsaturated lipids were not required for the tocopherol oxidase activity, but that lipids were necessary to provide an optimal, hydrophobic environment of the substrate for the reaction. The experiments on lipoxygenase and tocopherol oxidase activities in the leaves of light-grown P. coccineus plants during aging and during storage of the extracts from etiolated seedlings showed that the activity of the first reaction decreased considerably faster than the latter, indicating different mechanisms of both reactions performed by the same enzyme. As LOX3 was shown to occur in the apoplast of the related species P. vulgaris, the question as to the physiological function of LOX3 in the tocopherol oxidation activity in P. coccineus is discussed.

Reconstitution of the in vitro STUB1-mediated ubiquitination reaction system for α-1 antitrypsin mutant Z protein

The α-1 antitrypsin Z-mutant protein (ATZ) is the primary cause of α-1 antitrypsin deficiency (AATD). Studying the ubiquitination modification and degradation of ATZ protein is importance for developing treatments for AATD. STUB1 is an important E3 ubiquitin ligase that regulates ubiquitination modification of various proteins. However, whether STUB1 in involved in the ubiquitination modification of ATZ has not been fully elucidated. In this study, the ATZ and STUB1 coding genes were first cloned into the pET28a plasmid, constructing 2 protein expression plasmids. The recombinant plasmids were then transferred into the Escherichia coli for expression. With the optimization of induction temperature and IPTG dosage, the recombinant proteins were successfully expressed. The target proteins were then efficiently purified from cell lysates using metal-chelating affinity chromatography, and the accuracy of the amino acid sequence was verified through protein mass spectrometry analysis. Using the purified ATZ and STUB1, we established an in vitro ubiquitination reaction system. Experimental results showed that, in the presence of ATP, E1 ubiquitin-activating enzyme, and E2 ubiquitin-conjugating enzyme, STUB1 catalyzed the ubiquitination modification of ATZ. This study provides a method for obtaining the ATZ protein in vitro, elucidates the mechanism of STUB1 mediating ATZ ubiquitination, thereby advancing our understanding of the intracellular degradation mechanism of the α-1 antitrypsin Z-mutant.

Direct Injection Electrospray Ionization Mass Spectrometry (ESI-MS) Analysis of Proteins with High Matrix Content:Utilizing Taylor-Aris Dispersion.

This is the first work demonstrating the utility of the Taylor-Aris (TA) dispersion in avoiding serious interference issues commonly occurring in the electrospray ionization-mass spectrometric (ESI-MS) determination of therapeutic protein pharmaceuticals undergoing no pre-separation or sample purification. It was also pointed out that the TA dispersion conditions and its analytical utilization for proteomics can be easily accomplished in a commercial CE-MS instrument. In the proposed Taylor-Aris dispersion-assisted mass spectrometry (TADA-MS) analysis 0.5 μL sample is injected into a 65 cm long 50 μm i.d. capillary and pumped with 1 bar toward the MS. The procedure is efficient for the direct injection analysis of components having low diffusion coefficients (proteins) that are present in complex matrices of small organic and inorganic compounds.

Direct Injection Electrospray Ionization Mass Spectrometry (ESI‐MS) Analysis of Proteins with High Matrix Content:Utilizing Taylor–Aris Dispersion

AbstractThis is the first work demonstrating the utility of the Taylor–Aris (TA) dispersion in avoiding serious interference issues commonly occurring in the electrospray ionization‐mass spectrometric (ESI‐MS) determination of therapeutic protein pharmaceuticals undergoing no pre‐separation or sample purification. It was also pointed out that the TA dispersion conditions and its analytical utilization for proteomics can be easily accomplished in a commercial CE‐MS instrument. In the proposed Taylor–Aris dispersion‐assisted mass spectrometry (TADA‐MS) analysis 0.5 μL sample is injected into a 65 cm long 50 μm i.d. capillary and pumped with 1 bar toward the MS. The procedure is efficient for the direct injection analysis of components having low diffusion coefficients (proteins) that are present in complex matrices of small organic and inorganic compounds.

Mass Spectrometry of Putrescine, Spermidine, and Spermine Covalently Attached to Francisella tularensis Universal Stress Protein and Bovine Albumin.

Bacterial and mammalian cells are rich in putrescine, spermidine, and spermine. Polyamines are required for optimum fitness, but the biological function of these small aliphatic compounds has only been partially revealed. Known functions of polyamines include interaction with nucleic acids that alters gene expression and with proteins that modulate activity. Although polyamines can be incorporated into proteins, very few naturally occurring polyaminated proteins have been identified, which is due in part to the difficulty in detecting these adducts. In the current study, bovine albumin and the recombinant universal stress protein from Francisella tularensis were used as models for mass spectrometry analysis of polyaminated proteins. The proteins were covalently bound to putrescine, spermidine, or spermine by the action of carbodiimide or microbial transglutaminase. Tryptic peptides, subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS), were identified using Protein Prospector software. We describe the search parameters for identifying polyaminated peptides and show MS/MS spectra for adducts with putrescine, spermidine, and spermine. Manual evaluation led us to recognize signature ions for polyamine adducts on aspartate, glutamate, and glutamine, as well as neutral loss from putrescine, spermidine, and spermine during the fragmentation process. Mechanisms for the formation of signature ions and neutral loss are presented. Manual evaluation identified a false-positive adduct that had formed during trypsinolysis and resulted in peptide sequence rearrangement. Another false positive initially appeared to be a 71 kDa putrescine adduct on a cysteine residue. However, it was an acrylamide adduct on cysteine for a sample extracted from a polyacrylamide gel. The information presented in this report provides guidance and serves as a model for identifying naturally occurring polyaminated proteins.

A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum.

The common oral microbe Fusobacterium nucleatum has recently drawn attention after it was found to colonize tumors throughout the human body. Fusobacteria are also interesting study systems for bacterial RNA biology as these early-branching species encode many small noncoding RNAs (sRNAs) but lack homologs of the common RNA-binding proteins (RBPs) CsrA, Hfq and ProQ. To search for alternate sRNA-associated RBPs in F. nucleatum, we performed a systematic mass spectrometry analysis of proteins that co-purified with 19 different sRNAs. This approach revealed strong enrichment of the KH domain proteins KhpA and KhpB with nearly all tested sRNAs, including the σE-dependent sRNA FoxI, a regulator of several envelope proteins. KhpA/B act as a dimer to bind sRNAs with low micromolar affinity and influence the stability of several of their target transcripts. Transcriptome studies combined with biochemical and genetic analyses suggest that KhpA/B have several physiological functions, including being required for ethanolamine utilization. Our RBP search and the discovery of KhpA/B as major RBPs in F. nucleatum are important first steps in identifying key players of post-transcriptional control at the root of the bacterial phylogenetic tree.

Exploration of the biodegradation pathway and enhanced removal of imazethapyr from soil by immobilized Bacillus marcorestinctum YN1

Excessive or inappropriate applications of imazethapyr cause severe ecological deteriorations and health risks in human. A novel bacterial strain, i.e., Bacillus marcorestinctum YN1, was isolated to efficiently degrade imazethapyr, with the degradation pathways and intermediates predicted. Protein mass spectrometry analysis identified enzymes in strain YN1 potentially involved in imazethapyr biodegradation, including methylenetetrahydrofolate dehydrogenase, carbon-nitrogen family hydrolase, heme degrading monooxygenase, and cytochrome P450. The strain YN1 was further immobilized with biochar (BC600) prepared from mushroom waste (i.e., spent mushroom substrate) by pyrolysis at 600 °C to evaluate its degrading characteristics of imazethapyr. Scanning electron microscope observation showed that strain YN1 was adsorbed in the rich pore structure of BC600 and the adsorption efficiency reached the maximum level of 88.02% in 6 h. Both energy dispersive X-ray and Fourier transform infrared spectroscopy analyses showed that BC600 contained many elements and functional groups. The results of liquid chromatography showed that biochar-immobilized strain YN1 (IBC-YN1) improved the degradation rate of imazethapyr from 79.2% to 87.4%. The degradation rate of imazethapyr by IBC-YN1 could still reach 81.0% in the third recycle, while the bacterial survival rate was 67.73% after 180 d storage at 4 °C. The treatment of IBC-YN1 significantly shortened the half-life of imazethapyr in non-sterilized soil from 35.51 to 11.36 d, and the vegetative growth of imazethapyr sensitive crop plant (i.e., Cucumis sativus L.) was significantly increased in soil remediated, showing that the inhibition rate of root length and fresh weight were decreased by 12.45% and 38.49% respectively. This study exhanced our understanding of microbial catabolism of imazethapyr, and provided a potential in situ remediation strategy for improving the soil environment polluted by imazethapyr.

Mass Spectrometry Analysis of Shark Skin Proteins.

The mucus layer covering the skin of fish has several roles, including protection against pathogens and mechanical damage in which proteins play a key role. While proteins in the skin mucus layer of various common bony fish species have been explored, the proteins of shark skin mucus remain unexplored. In this pilot study, we examine the protein composition of the skin mucus in spiny dogfish sharks and chain catsharks through mass spectrometry (NanoLC-MS/MS). Overall, we identified 206 and 72 proteins in spiny dogfish (Squalus acanthias) and chain catsharks (Scyliorhinus retifer), respectively. Categorization showed that the proteins belonged to diverse biological processes and that most proteins were cellular albeit a significant minority were secreted, indicative of mucosal immune roles. The secreted proteins are reviewed in detail with emphasis on their immune potentials. Moreover, STRING protein-protein association network analysis showed that proteins of closely related shark species were more similar as compared to a more distantly related shark and a bony fish, although there were also significant overlaps. This study contributes to the growing field of molecular shark studies and provides a foundation for further research into the functional roles and potential human biomedical implications of shark skin mucus proteins.

CTGF promotes the repair and regeneration of alveoli after acute lung injury by promoting the proliferation of subpopulation of AEC2s

BackgroundFunctional alveolar regeneration is essential for the restoration of normal lung homeostasis after acute lung injury (ALI) and acute respiratory distress syndrome (ARDS). Lung is a relatively quiescent organ and a variety of stem cells are recruited to participate in lung repair and regeneration after lung tissue injury. However, there is still no effective method for promoting the proliferation of endogenous lung stem cells to promote repair and regeneration.MethodsUsing protein mass spectrometry analysis, we analyzed the microenvironment after acute lung injury. RNA sequencing and image cytometry were used in the alveolar epithelial type 2 cells (AEC2s) subgroup identification. Then we used Sftpc+AEC2 lineage tracking mice and purified AEC2s to further elucidate the molecular mechanism by which CTGF regulates AEC2s proliferation both in vitro and in vivo. Bronchoalveolar lavage fluid (BALF) from thirty ARDS patients who underwent bronchoalveolar lavage was collected for the analysis of the correlation between the expressing of Krt5 in BALF and patients’ prognosis.ResultsHere, we elucidate that AEC2s are the main facultative stem cells of the distal lung after ALI and ARDS. The increase of connective tissue growth factor (CTGF) in the microenvironment after ALI promoted the proliferation of AEC2s subpopulations. Proliferated AEC2s rapidly expanded and differentiated into alveolar epithelial type 1 cells (AEC1s) in the regeneration after ALI. CTGF initiates the phosphorylation of LRP6 by promoting the interaction between Krt5 and LRP6 of AEC2s, thus activating the Wnt signaling pathway, which is the molecular mechanism of CTGF promoting the proliferation of AEC2s subpopulation.ConclusionsOur study verifies that CTGF promotes the repair and regeneration of alveoli after acute lung injury by promoting the proliferation of AEC2s subpopulation.

New Insights into the Role of HMGB2 in ST-Segment Elevation Myocardial Infarction.

Ischemic heart disease is one of the leading causes of death in the world, of which ST-segment elevation myocardial infarction (STEMI) is an important type. Inappropriate activation and accumulation of platelets typically induced thrombosis, which may result in acute vessel occlusion and STEMI. Multiple cytokines have been shown to regulate platelet activation, but the relationship between HMGB2 and platelet activation has not been elucidated. We collected peripheral blood of STEMI patients and healthy adults, and mass spectrometry analysis of platelet proteins was conducted. The "edgeR" package was used to identify the differentially expressed proteins (DEPs). The Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene ontology (GO) and Gene Set Enrichment Analysis (GSEA) were used to identify the significantly changed pathways. Western blot and ELISA were used to detect the expression of a high mobility group box 2 (HMGB2). Flow cytometric analysis and platelet aggregation rate were performed to evaluate the activation of platelets. We identified ALOX5, HIST1H1B, S100A11, HMGB2, and RPS15A were the top five up-regulated proteins by differential expression analysis. Western blot verified that the relative protein expression of HMGB2 in platelet was significantly higher in STEMI patients compared with control adults, and the results of ELISA indicated that the serum HMGB2 level increased and significantly correlated with neutrophil count in STEMI patients. Further investigation showed that the platelet aggregation induced by ADP, the activation of integrin αIIbβ3 and CD62P expression on platelet surface were all enhanced by the recombinant HMGB2 (rHMGB2). In conclusion, HMGB2 may be the key molecule to regulate platelet activation in patients with STEMI, which may serve as a potential therapeutic target for STEMI.

The Mass Spectrometry Identification, Antimicrobial Genes Detection, and Proteomics Analysis of Stutzerimonas stutzeri Strain Was Isolated from Industrial Wastewater

A large amount of organic matter, heavy metals, and even antibiotics are present in industrial wastewater, aquaculture waters, and various types of sewage, along with abundant microorganisms. To date, only a few studies involving the resistance and proteomics of Stutzerimonas stutzeri in high-salt wastewater are available. Herein, a comprehensive assessment of a newly isolated Stutzerimonas stutzeri strain, which is present in high-salt wastewater, was performed using mass spectrometry, genetic identification, and biochemical analysis to characterize the genetic and biochemical properties. Growth experiments revealed that the Stutzerimonas stutzeri strain had a moderate growth rate in nutrient broth, and the bacterial count was not high. Further analysis highlighted an apparent susceptibility of this strain to most antibiotics but some resistance to chloramphenicol and minocycline. A resistance gene assay results showed that the gene gyrB was associated with antibiotic resistance in this Stutzerimonas stutzeri strain. Proteomic analysis revealed for the first time the co-existence of two drug-resistance-related proteins (Multidrug/solvent RND membrane fusion protein and MexE) in Stutzerimonas stutzeri. Moreover, Stutzerimonas stutzeri isolated from high-salt wastewater was subjected to drug resistance gene detection, and the total protein of Stutzerimonas stutzeri was detected by protein mass spectrometry analysis. The subcellular classification shows that the 50 proteins with the highest abundance are divided into cell inner membrane, cell outer membrane, cytoplasm, cytoplasmic side, membrane, multi-pass membrane protein, and peripheral membrane protein, among which the proportion of cytoplasmic components is the highest. Overall, this study’s findings provide a new perspective for further research on the characteristics of Stutzerimonas stutzeri in high-salt wastewater.

Bacillus sp. YC7 from intestines of Lasioderma serricorne degrades nicotine due to nicotine dehydrogenase

A large number of nicotine-containing wastes produced during the tobacco manufacturing process are seriously harmful to the environment and human health. The degradation and transformation of nicotine-containing environmental contaminants to harmless substances has become an urgent requirement. Lasioderma serricorne can grow and reproduce in nicotine-rich sources, and their intestinal microbiota show promising potential to degrade and utilize nicotine. The purpose of this study is to screen and identify nicotine-degrading bacteria from the intestines of L. serricorne and explore their degradation characteristics. A dominant strain, YC7, with significant nicotine degradation capabilities was isolated from the intestines of L. serricorne. The strain was identified as Bacillus using a polyphasic approach. The test results showed it can produce multiple enzymes that include β-glucosidase, cellulase, proteases, and amylases. The nicotine-degrading bacteria were functionally annotated using databases. Nicotine dehydrogenase (NDH) was found by combining an activity tracking test and protein mass spectrometry analysis. The YC-7 NDH in the pathway was molecularly docked and functionally verified via the gene knockdown method. The binding ability of nicotine to nicotine-degrading enzymes was investigated using molecular docking. A high-efficiency nicotine-degrading bacteria, YC-7, was isolated and screened from tobacco, and the gene functions related to degradation were verified. This investigation provides a new hypothesis for screening nicotine-degrading bacteria and increases our knowledge of potential nicotine-degrading microbial sources.

Crown-of-thorns starfish spines secrete defence proteins.

The crown-of-thorns starfish (COTS; Acanthaster species) is a slow-moving corallivore protected by an extensive array of long, sharp toxic spines. Envenomation can result in nausea, numbness, vomiting, joint aches and sometimes paralysis. Small molecule saponins and the plancitoxin proteins have been implicated in COTS toxicity. Brine shrimp lethality assays were used to confirm the secretion of spine toxin biomolecules. Histological analysis, followed by spine-derived proteomics helped to explain the source and identity of proteins, while quantitative RNA-sequencing and phylogeny confirmed target gene expression and relative conservation, respectively. We demonstrate the lethality of COTS spine secreted biomolecules on brine shrimp, including significant toxicity using aboral spine semi-purifications of >10 kDa (p>0.05, 9.82 µg/ml), supporting the presence of secreted proteins as toxins. Ultrastructure observations of the COTS aboral spine showed the presence of pores that could facilitate the distribution of secreted proteins. Subsequent purification and mass spectrometry analysis of spine-derived proteins identified numerous secretory proteins, including plancitoxins, as well as those with relatively high gene expression in spines, including phospholipase A2, protease inhibitor 16-like protein, ependymin-related proteins and those uncharacterized. Some secretory proteins (e.g., vitellogenin and deleted in malignant brain tumor protein 1) were not highly expressed in spine tissue, yet the spine may serve as a storage or release site. This study contributes to our understanding of the COTS through functional, ultrastructural and proteomic analysis of aboral spines.

Improving mass accuracy in matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis of pathogenic proteins using 6xHIS-tagged internal calibration.

Linear mode of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOFMS) has been routinely used for bacterial identification in the clinic, depending on the pattern analysis of spectral libraries rather than accurate mass measurement of ribosomal proteins (10-15 kDa). However, a demand for more accurate mass analysis of pathogens (e.g. KPC-2 carbapenemase) has been recently increasing for diagnostic purposes. We introduced a 6xHIS-tagged KPC-2 (i.e. hKPC-2) and used it as an internal mass calibrator for the mass calibration of target proteins. After internal mass calibration (In-Cal), we evaluated the observed mass of KPC-2 against the theoretical mass of hKPC-2, which has 823 Da mass difference from the target protein. We further assessed the accuracy and precision of our calibration method regarding the identification of KPC-2 and other pathogens in clinical isolates (n = 42). Among several candidates for internal mass calibrators, the In-Cal using a 6xHIS-tagged protein on the target showed the highest mass accuracy and precision in the detection of target proteins (e.g. KPC-2). The application of hKPC-2 as an internal calibrator showed substantial improvement of mass accuracy, mass precision and also quantification of KPC in linearity and repeatability for KPC detection in the clinical isolates. Our In-Cal method using 6xHIS-tagged protein in MALDI-TOFMS allows successful mass calibration (<3.5Da) of pathogenic proteins (>20 kDa) and provides high mass accuracy as much as that of medium- and high-resolution mass spectrometry.