Comparative proteomics reveals the response and adaptation mechanisms of white Hypsizygus marmoreus against the biological stress caused by Penicillium

White Hypsizygus marmoreus is a popular edible mushroom.Its mycelium is easy to be contaminated by Penicillium,which leads to a decrease in its quality and yield.Penicillium could compete for limited space and nutrients through rapid growth and produce a variety of harmful gases,such as benzene,aldehydes,phenols,etc.,to inhibit the growth of H.marmoreus mycelium.A series of changes occurred in H.marmoreus proteome after contamination when detected by the label-free tandem mass spectrometry(MS/MS)technique.Some proteins with up-regulated expression worked together to participate in some processes,such as the non-toxic transformation of harmful gases,glutathione metabolism,histone modification,nucleotide excision repair,clearing misfolded proteins,and synthesizing glutamine,which were mainly used in response to biological stress.The proteins with down-regulated expression are mainly related to the processes of ribosome function,protein processing,spliceosome,carbon metabolism,glycolysis,and gluconeogenesis.The reduction in the function of these proteins affected the production of the cell components,which might be an adjustment to adapt to growth retardation.This study further enhanced the understanding of the biological stress response and the growth restriction adaptation mechanisms in edible fungi.It also provided a theoretical basis for protein function exploration and edible mushroom food safety research.

Global and Comparative Proteome Analysis of Nitrogen-Stress Responsive Proteins in the Root, Stem and Leaf of Brassica napus

Nitrogen(N)is one of the basic nutrients and signals for plant development and deficiency of it would always limit the productions of crops in the field.Quantitative research on expression of N-stress responsive proteins on a proteome level remains elusive.In order to gain a deep insight into the proteins responding to nitrogen stress in rapeseed(Brassica napus L.),comparative proteomic analysis was performed to investigate changes of protein expression profiles from the root,stem and leaf under different N concentrations,respectively.More than 200 differential abundance proteins(DAPs)were detected and categorized into groups according to annotations,including“binding and catalytic activity”,“involved in primary metabolism and cellular processes”,“stress-response”and so on.Variation in chlorophyll(Chl)content and antioxidant activities further revealed that oxidative stress raised with the increase of N concentration.Bioinformatics analysis based on the expression level of total proteins suggested these DAPs might play important roles in adaptation to N-stress conditions.Generally,these results provides a new aspect into N-stress responding proteins in Brassica plants.

Differentially expressed whey proteins of donkey and bovine colostrum revealed with a label-free proteomics approach

This study aimed to analyze and compare the differentially expressed whey proteins(DEWPs)of donkey and bovine colostrum using high-performance liquid chromatography with tandem mass spectrometry-based proteomics.A total of 620 and 696 whey proteins were characterized in the donkey and bovine colostrum,respectively,including 383 common whey proteins.Among these common proteins,80 were identified as DEWPs,including 21 upregulated and 59 downregulated DEWPs in donkey colostrum compared to bovine colostrum.Gene Ontology analysis revealed that these DEWPs were mainly related to cellular components,such as extracellular exosome,plasma membrane,and mitochondrion;biological processes,such as oxidation-reduction process,cell-cell adhesion,and small guanosine triphosphate(GTP)ase-mediated signal transduction;and molecular functions,such as GTP binding,GTPase activity,and soluble N-ethylmaleimide-sensitive factor(NSF)attachment protein receptor activity.Metabolic pathway analysis suggested that the majority of the DEWPs were associated with soluble NSF factor attachment protein receptor interactions in vesicular transport,fatty acid biosynthesis,and estrogen signaling pathways.Our results provide a vital insight into the differences between donkey and bovine colostrum,along with important information on the significant components as nutritional and functional factors to be included in infant formula based on multiple milk sources.

Identification of Annexin A1 protein expression in human gastric adenocarcinoma using proteomics and tissue microarray

AIM:To study the differential expression of Annexin A1(ANXA1)protein in human gastric adenocarcinoma.This study was also designed to analyze the relationship between ANXA1 expression and the clinicopathological parameters of gastric carcinoma.METHODS:Purified gastric adenocarcinoma cells(GAC)and normal gastric epithelial cells(NGEC)were obtained from 15 patients with gastric cancer by laser capture microdissection.All of the peptide specimens were labeled as18O/16O after trypsin digestion.Differential protein expressions were quantitatively identified between GAC and NGEC by nanoliter-reverse-phase liquid chromatography-mass/mass spectrometry(nanoRPLC-MS/MS).The expressions of ANXA1 in GAC and NGEC were verified by western blot analysis.The tissue microarray containing the expressed ANXA1 in 75 pairs of gastric carcinoma and paracarcinoma specimens was detected by immunohistochemistry(IHC).The relationship between ANXA1 expression and clinicopathological parametes of gastric carcinoma was analyzed.RESULTS:A total of 78 differential proteins were identified.Western blotting revealed that ANXA1 expression was significantly upregulated in GAC(2.17/1,P<0.01).IHC results showed the correlations between ANXA1protein expression and the clinicopathological parameters,including invasive depth(T stage),lymph node metastasis(N stage),distant metastasis(M stage)and tumour-lymph node metastasis stage(P<0.01).However,the correlations between ANXA1 protein expression and the remaining clinicopathological parameters,including sex,age,histological differentiation and the size of tumour were not found(P>0.05).CONCLUSION:The upregulated ANXA1 expression may be associated with carcinogenesis,progression,invasion and metastasis of GAC.This protein could be considered as a biomarker of clinical prognostic prediction and targeted therapy of GAC.

Proteomics of the mediodorsal thalamic nucleus of rats with stress-induced gastric ulcer

BACKGROUND Stress-induced gastric ulcer(SGU) is one of the most common visceral complications after trauma. Restraint water-immersion stress(RWIS) can cause serious gastrointestinal dysfunction and has been widely used to study the pathogenesis of SGU to identify medications that can cure the disease. The mediodorsal thalamic nucleus(MD) is the centre integrating visceral and physical activity and contributes to SGU induced by RWIS. Hence, the role of the MD during RWIS needs to be studied.AIM To screen for differentially expressed proteins in the MD of the RWIS rats to further elucidate molecular mechanisms of SGU.METHODS Male Wistar rats were selected randomly and divided into two groups, namely, a control group and an RWIS group. Gastric mucosal lesions of the sacrificed rats were measured using the erosion index and the proteomic profiles of the MD were generated through isobaric tags for relative and absolute quantitation(iTRAQ) coupled with two-dimensional liquid chromatography and tandem mass spectrometry. Additionally, iTRAQ results were verified by Western blot analysis.RESULTS A total of 2853 proteins were identified, and these included 65 dysregulated(31 upregulated and 34 downregulated) proteins(fold change ratio ≥ 1.2). Gene Ontology(GO) analysis showed that most of the upregulated proteins are primarily related to cell division, whereas most of the downregulated proteins are related to neuron morphogenesis and neurotransmitter regulation. Ingenuity Pathway Analysis revealed that the dysregulated proteins are mainly involved in the neurological disease signalling pathways. Furthermore, our results indicated that glycogen synthase kinase-3 beta might be related to the central mechanismthrough which RWIS gives rise to SGU.CONCLUSION Quantitative proteomic analysis elucidated the molecular targets associated with the production of SGU and provides insights into the role of the MD. The underlying molecular mechanisms need to be further dissected.

Circulating proteomic biomarkers for diagnosing sporadic amyotrophic lateral sclerosis:a cross-sectional study

Biomarke rs are required for the early detection,prognosis prediction,and monitoring of amyotrophic lateral sclerosis,a progressive disease.Proteomics is an unbiased and quantitative method that can be used to detect neurochemical signatures to aid in the identification of candidate biomarke rs.In this study,we used a label-free quantitative proteomics approach to screen for substantially differentially regulated proteins in ten patients with sporadic amyotrophic lateral scle rosis compared with five healthy controls.Su bstantial upregulation of serum proteins related to multiple functional clusters was observed in patients with spo radic amyotrophic lateral sclerosis.Potential biomarke rs were selected based on functionality and expression specificity.To validate the proteomics profiles,blood samples from an additional cohort comprising 100 patients with sporadic amyotrophic lateral sclerosis and 100 healthy controls were subjected to enzyme-linked immunosorbent assay.Eight substantially upregulated serum proteins in patients with spora dic amyotrophic lateral sclerosis were selected,of which the cathelicidin-related antimicrobial peptide demonstrated the best discriminative ability between patients with sporadic amyotrophic lateral sclerosis and healthy controls(area under the curve[AUC]=0.713,P<0.0001).To further enhance diagnostic accuracy,a multi-protein combined discriminant algorithm was developed incorporating five proteins(hemoglobin beta,cathelicidin-related antimicrobial peptide,talin-1,zyxin,and translationally-controlled tumor protein).The algo rithm achieved an AUC of 0.811 and a P-value of<0.0001,resulting in 79%sensitivity and 71%specificity for the diagnosis of sporadic amyotrophic lateral scle rosis.Subsequently,the ability of candidate biomarkers to discriminate between early-stage amyotrophic lateral sclerosis patients and controls,as well as patients with different disease severities,was examined.A two-protein panel comprising talin-1 and translationally-controlled tumor protein effectively distinguished early-stage amyotrophic lateral sclerosis patients from controls(AUC=0.766,P<0.0001).Moreove r,the expression of three proteins(FK506 binding protein 1A,cathelicidin-related antimicrobial peptide,and hemoglobin beta-1)was found to increase with disease progression.The proteomic signatures developed in this study may help facilitate early diagnosis and monitor the progression of sporadic amyotrophic lateral sclerosis when used in co mbination with curre nt clinical-based parameters.

Comprehensive and deep profiling of the plasma proteome with protein corona on zeolite NaY

Proteomic characterization of plasma is critical for the development of novel pharmacodynamic biomarkers.However,the vast dynamic range renders the profiling of proteomes extremely challenging.Here,we synthesized zeolite NaY and developed a simple and rapid method to achieve comprehensive and deep profiling of the plasma proteome using the plasma protein corona formed on zeolite NaY.Specifically,zeolite NaY and plasma were co-incubated to form plasma protein corona on zeolite NaY(NaY-PPC),followed by conventional protein identification using liquid chromatography-tandem mass spectrometry.NaY was able to significantly enhance the detection of low-abundance plasma proteins,minimizing the“masking”effect caused by high-abundance proteins.The relative abundance of middleand low-abundance proteins increased substantially from 2.54%to 54.41%,and the top 20 highabundance proteins decreased from 83.63%to 25.77%.Notably,our method can quantify approximately 4000 plasma proteins with sensitivity up to pg/mL,compared to only about 600 proteins identified from untreated plasma samples.A pilot study based on plasma samples from 30 lung adenocarcinoma patients and 15 healthy subjects demonstrated that our method could successfully distinguish between healthy and disease states.In summary,this work provides an advantageous tool for the exploration of plasma proteomics and its translational applications.

The pathogenic mechanism of TAR DNA-binding protein 43(TDP-43)in amyotrophic lateral sclerosis

The onset of amyotrophic lateral sclerosis is usually characterized by focal death of both upper and/or lower motor neurons occurring in the motor cortex,basal ganglia,brainstem,and spinal cord,and commonly involves the muscles of the upper and/or lower extremities,and the muscles of the bulbar and/or respiratory regions.However,as the disease progresses,it affects the adjacent body regions,leading to generalized muscle weakness,occasionally along with memory,cognitive,behavioral,and language impairments;respiratory dysfunction occurs at the final stage of the disease.The disease has a complicated pathophysiology and currently,only riluzole,edaravone,and phenylbutyrate/taurursodiol are licensed to treat amyotrophic lateral sclerosis in many industrialized countries.The TAR DNA-binding protein 43 inclusions are observed in 97%of those diagnosed with amyotrophic lateral sclerosis.This review provides a preliminary overview of the potential effects of TAR DNAbinding protein 43 in the pathogenesis of amyotrophic lateral sclerosis,including the abnormalities in nucleoplasmic transport,RNA function,post-translational modification,liquid-liquid phase separation,stress granules,mitochondrial dysfunction,oxidative stress,axonal transport,protein quality control system,and non-cellular autonomous functions(e.g.,glial cell functions and prion-like propagation).

Biochanin A attenuates spinal cord injury in rats during early stages by inhibiting oxidative stress and inflammasome activation

Previous studies have shown that Biochanin A,a flavonoid compound with estrogenic effects,can serve as a neuroprotective agent in the context of cerebral ischemia/reperfusion injury;howeve r,its effect on spinal cord injury is still unclea r. In this study,a rat model of spinal cord injury was established using the heavy o bject impact method,and the rats were then treated with Biochanin A(40 mg/kg) via intrape ritoneal injection for 14 consecutive days.The res ults showed that Biochanin A effectively alleviated spinal cord neuronal injury and spinal co rd tissue injury,reduced inflammation and oxidative stress in spinal cord neuro ns,and reduced apoptosis and pyroptosis.In addition,Biochanin A inhibited the expression of inflammasome-related proteins(ASC,NLRP3,and GSDMD)and the Toll-like receptor 4/nuclear factor-κB pathway,activated the Nrf2/heme oxygenase 1 signaling pathway,and increased the expression of the autophagy markers LC3 Ⅱ,Beclin-1,and P62.Moreove r,the therapeutic effects of Biochanin A on early post-s pinal cord injury were similar to those of methylprednisolone.These findings suggest that Biochanin A protected neurons in the injured spinal cord through the Toll-like receptor 4/nuclear factor κB and Nrf2/heme oxygenase 1 signaling pathways.These findings suggest that Biochanin A can alleviate post-spinal cord injury at an early stage.

Electroacupuncture pretreatment exhibits antidepressive effects by regulating hippocampal proteomics in rats with chronic restraint stress

The clinical effect of electroacupuncture on depression is widely recognized. However, the signal transduction pathways and target proteins involved remain unclear. In the present study, rat models of chronic restraint stress were used to explore the mechanism by which electroacupuncture alleviates depression. Rats were randomly divided into control, model, and electroacupuncture groups. Chronic restraint stress was induced in the model and electroacupuncture groups by restraining rats for 28 days. In the electroacupuncture group, electroacupuncture pretreatment at Baihui（GV20） and Yintang（GV29） acupoints was performed daily（1 m A, 2 Hz, discontinuous wave, 20 minutes） prior to restraint for 28 days. Open field tests and body weight measurements were carried out to evaluate the depressive symptoms at specific time points. On day 28, the crossing number, rearing number, and body weights of the model group were significantly lower than those in the control group. Behavior test results indicated that rat models of depressive-like symptoms were successfully established by chronic restraint stress combined with solitary raising. On day 28, an isobaric tag for a relative and absolute quantitation-based quantitative proteomic approach was performed to identify differentially expressed proteins in hippocampal samples obtained from the model and electroacupuncture groups. The potential function of these differential proteins was predicted through the use of the Cluster of Orthologous Groups of proteins（COG） database. Twenty-seven differential proteins（uncharacteristic proteins expected） were selected from the model and electroacupuncture groups. In addition to unknown protein functions, COG are mainly concentrated in general prediction function, mechanism of signal transduction, amino acid transport and metabolism groups. This suggests that electroacupuncture improved depressive-like symptoms by regulating differential proteins, and most of these related proteins exist in nerve cells.

iTRAQ-Based Proteomics Investigation of Critical Response Proteins in Embryo and Coleoptile During Rice Anaerobic Germination

Direct-seeding of rice has become popular in recent years due to its low cost and convenience,however,hypoxic condition limits seedling establishment.In this study,weedy rice WR04-6 with high germination ability under anaerobic conditions was used as a gene donor,and we successfully improved the seedling establishment rate of rice cultivar Qishanzhan(QSZ)based on selection of a new rice line R42 from the recombinant inbred line population.R42 inherited high anaerobic germination(AG)ability,and was used for isobaric tags for relative and absolute quantitation(iTRAQ)-based comparative proteomic studies with QSZ to further explore the molecular mechanism of AG.A total of 719 differentially abundant proteins(DAPs)were shared by R42 and QSZ responded to AG,and thus defined as common response DAPs.A total of 300 DAPs that responded to AG were only identified from R42,which were defined as tolerance-specific DAPs.The common response and tolerance-specific DAPs had similar biochemical reaction processes and metabolic pathways in response to anoxic stress,however,they involved different proteins.The tolerance-specific DAPs were involved in amino acid metabolism,starch and sucrose metabolism,tricarboxylic acid cycle pathway,ethylene synthesis pathway,cell wall-associated proteins and activity of active oxygen scavenging enzyme.The in silico protein-protein interactions for the top 60 DAPs indicated that tolerance-specific DAPs had relatively independent protein interaction networks in response to an anoxic environment compared with common response DAPs.The results of physiological indicators showed thatα-amylase and superoxide dismutase activities of R42 were significantly increased under anoxic conditions compared with aerobic conditions.Multiple lines of evidence from western blot,physiological analysis and quantitatDirect seeding of rice has become popular in recent years due to its low cost and convenience,however,hypoxic conditions can limit seedling establishment.In the present study,weedy rice WR04-6 with high germination ability in anaerobic conditions was used as the gene donor and successfully improved the seedling establishment rate of rice cultivar Qishanzhan(QSZ)based on selection of a new rice line R42 from the recombinant inbred line(RIL)population.R42 inherited the had high anaerobic germination(AG)ability,which was used for the isobaric tags for relative and absolute quantitation(iTRAQ)based comparative proteomic studies with QSZ to further explore the molecular mechanism of AG.A total of 719 differentially abundant proteins(DAPs)shared by R42 and QSZ responded to AG and were thus defined as common response DAPs.A total of 300 DAPs that responded to AG were only identified from R42,which were defined as tolerance-specific DAPs.The common response and tolerance-specific DAPs had similar biochemical reaction processes and metabolic pathways in response to anoxic stress,however they involved different proteins.The 300 tolerance-specific DAPs were involved in amino acid metabolism,starch and sucrose metabolism,TCA cycle pathways,ethylene synthesis pathway,cell wall-associated proteins and activity of active oxygen scavenging enzyme.The in silico protein-protein interactions for the top 60 DAPs indicated that tolerance-specific DAPs had relatively independent protein interaction networks in response to an anoxic environment compared with common response DAPs.The results of physiological indicators showed thatα-amylase and SOD activities of R42 were significantly increased under anoxic conditions compared with aerobic conditions.Multiple lines of evidence from western blot,physiological analyses and real-time PCR jointly supported the reliability of proteomics data.In summary,our findings deepened the understanding of the molecular mechanism for the rice response to AG.ive real-time PCR jointly supported the reliability of proteomics data.In summary,our findings deepened the understanding of the molecular mechanism for the rice response to AG.

Charcot-Marie-Tooth-1A and sciatic nerve crush rat models:insights from proteomics

The sensorimotor and histological aspects of peripheral neuropathies were already studied by our team in two rat models:the sciatic nerve crush and the Charcot-Marie-Tooth-1A disease.In this study,we sought to highlight and compare the protein signature of these two pathological situations.Indeed,the identification of protein profiles in diseases can play an important role in the development of pharmacological targets.In fact,Charcot-Marie-Tooth-1A rats develop motor impairments that are more severe in the hind limbs.Therefore,for the first time,protein expression in sciatic nerve of Charcot-Marie-Tooth-1A rats was examined.First,distal sciatic nerves were collected from Charcot-Marie-Tooth-1A and uninjured wild-type rats aged 3 months.After protein extraction,sequential window acquisition of all theoretical fragment ion spectra liquid chromatography and mass spectrometry was employed.445 proteins mapped to Swiss-Prot or trEMBL Uniprot databases were identified and quantified.Of these,153 proteins showed statistically significant differences between Charcot-Marie-Tooth-1A and wild-type groups.The majority of these proteins were overexpressed in Charcot-Marie-Tooth-1A.Hierarchical clustering and functional enrichment using Gene Ontology were used to group these proteins based on their biological effects concerning Charcot-Marie-Tooth-1A pathophysiology.Second,proteomic characterization of wild-type rats subjected to sciatic nerve crush was performed sequential window acquisition of all theoretical fragment ion spectra liquid chromatography and mass spectrometry.One month after injury,distal sciatic nerves were collected and analyzed as described above.Out of 459 identified proteins,92 showed significant differences between sciatic nerve crush and the uninjured wild-type rats used in the first study.The results suggest that young adult Charcot-Marie-Tooth-1A rats(3 months old)develop compensatory mechanisms at the level of redox balance,protein folding,myelination,and axonogenesis.These mechanisms seem insufficient to hurdle the progress of the disease.Notably,response to oxidative stress appears to be a significant feature of Charcot-Marie-Tooth-1A,potentially playing a role in the pathological process.In contrast to the first experiment,the majority of the proteins that differed from wild-type were downregulated in the sciatic nerve crush group.Functional enrichment suggested that neurogenesis,response to axon injury,and oxidative stress were important biological processes.Protein analysis revealed an imperfect repair at this time point after injury and identified several distinguishable proteins.In conclusion,we suggest that peripheral neuropathies,whether of a genetic or traumatic cause,share some common pathological pathways.This study may provide directions for better characterization of these models and/or identifying new specific therapeutic targets.

GhHSP24.7 mediates mitochondrial protein acetylation to regulate stomatal conductance in response to abiotic stress in cotton

During seed germination,the cotton chaperone protein HSP24.7 regulates the release,from the mitochondrial electron transport chain,of reactive oxygen species(ROS),a stimulative signal regulating germination.The function of HSP24.7 during vegetative stages remains largely unknown.Here we propose that suppression of Gh HSP24.7 in cotton seedlings increases tolerance to heat and drought stress.Elevation of Gh HSP24.7 was found to be positively associated with endogenous levels of ROS.We identified a new client protein of Gh HSP24.7,cotton lysine deacetylase(Gh HDA14),which is involved in mitochondrial protein modification.Elevated levels of Gh HSP24.7 suppressed deacetylase activity in mitochondria,leading to increased acetylation of mitochondrial proteins enriched in the subunit of Ftype ATPase,V-type ATPase,and cytochrome C reductase,ultimately reducing leaf ATP content.Consequently,in combination with altered ROS content,Gh HSP24.7 transgenic lines were unable to coordinate stomatal closure under stress.The regulation circuit composed of Gh HSP24.7 and Gh HDA14 represents a post-translation level mechanism in plant abiotic stress responses that integrates the regulation of ROS and ATP.

Proteomics identifies a novel role of fibrinogen-like protein 1 in Crohn’s disease

BACKGROUND Crohn’s disease(CD)is an incurable intestinal disorder with unclear etiology and pathogenesis.Currently,there is a lack of specific biomarkers and drug targets for CD in clinical practice.It is essential to identify the precise pathophysiological mechanism of CD and investigate new therapeutic targets.AIM To explore a new biomarker and therapeutic target for CD and verify its role in the CD pathological mechanism.METHODS Proteomics was performed to quantify the protein profile in the plasma of 20 CD patients and 20 matched healthy controls.Hub genes among the selected differentially expressed proteins(DEPs)were detected via the MCODE plugin in Cytoscape software.The expression level of one hub gene with an immunoregulatory role that interested us was verified in the inflamed intestinal tissues of 20 CD patients by immunohistochemical analysis.After that,the effects of the selected hub gene on the intestinal inflammation of CD were identified in a CD cell model by examining the levels of proinflammatory cytokines by enzymelinked immunosorbent assays and the expression of the NF-κB signalling pathway by quantitative real-time PCR analysis and Western blot assays.RESULTS Thirty-five DEPs were selected from 393 credible proteins identified by proteomic analysis.Among the DEPs,fibrinogen-like protein 1(FGL1),which attracted our attention due to its function in the regulation of the immune response,had 1.722-fold higher expression in the plasma of CD patients and was identified as a hub gene by MCODE.Furthermore,the expression of FGL1 in the intestinal mucosal and epithelial tissues of CD patients was also upregulated(P<0.05).In vitro,the mRNA levels of FGL1 and NF-κB;the protein expression levels of FGL1,IKKα,IKKβ,p-IKKα/β,p-IκBα,and p-p65;and the concentrations of the proinflammatory cytokines IL-1β,IL-6,IL-17,and TNF-αwere increased(P<0.05)after stimulation with lipopolysaccharide,which were reversed by knockdown of FGL1 with siRNA transfection(P<0.05).Conversely,FGL1 overexpression enhanced the abovementioned results(P<0.05).CONCLUSION FGL1 can induce intestinal inflammation by activating the canonical NF-κB signalling pathway,and it may be considered a potential biomarker and therapeutic target for CD.

Proteomic Analysis of High Temperature Stress-Responsive Proteins in Chrysanthemum Leaves

Chrysanthemum is one of the most important ornamental flowers in the world,and temperature has a significant influence on its field production.In the present study,differentially expressed proteins were investigated in the leaves of Dendranthema grandiflorum‘Jinba’under high temperature stress using label-free quantitative proteomics techniques.The expressed proteins were comparatively identified and analyzed.A total of 1,463 heat-related,differentially expressed proteins were successfully identified by Liquid Chromatography-tandem Mass Spectrometry(LC-MS/MS),and 1,463 heat-related,differentially expressed proteins were successfully identified by mass spectrometry after a high temperature treatment.Among these,701 proteins were upregulated and 762 proteins were downregulated.The in-depth bioinformatics analysis of these differentially expressed proteins revealed that these were involved in energy metabolism pathways,protein metabolism,and heat shock.In the present study,the investigators determined the changes in the levels of some proteins,and their expression at the protein and molecular levels in chrysanthemum to help reveal the mechanism of heat resistance in chrysanthemum.Furthermore,the present study elucidated some of the proteins correlated to heat resistance in chrysanthemum,and their expression changes at the protein and molecular levels to help reveal the mechanism of heat resistance in this flower species.These results provide a theoretical basis for the selection of new heat resistant varieties of chrysanthemum in the field.

Proteomics-based analysis of functional proteins from fermented of compound wheat embryo Chinese medicine

Compound probiotics were used to ferment compound wheat embryo Chinesemedicine(CWECM)at 37°C for a given period,and the fermentation end pointwas determined based on pHvalue.The full spectrumof the proteinswithin the fermentation supernatant was determined by ion mass spectrometry,and then the fermentation was analyzed by proteomics.The difference of functional protein ofCWECMwas analyzed before and after fermentation.Additionally,the changes in flavor of peptides were examined.Our results indicated that when the fermentationwas performed for 96 h,the pH value became stable over time,which it shifted froman initial 3.98±0.04 to a stable 2.78±0.04.Proteomicbased analysis of the fermentation supernatant indicated that the fermentation of the probiotics increased.The amount of functional proteome and protein within the supernatant increased from 60 proteomes and 136 proteins before fermentation to 70 proteomes and 149 proteins post fermentation.These proteins were primarily members of the Ubiquitin and Histone families.These families contain more specific peptides after fermentation,and the coverage was reduced.Analysis of the unique P0C512 protein after fermentation indicated that this protein is an unstable,3Deffect columnar protein.We also found that probiotic fermentation can reduce the proportion of bitter peptideswithin fermentation broth from 47.49%to 36.98%,and the proportion of sweet peptides increased after fermentation from 35.29%to 51.01%.Based on testing,we concluded that fermentation of CWECM by compound probiotics can reduce the pH of the CWECM solution,increase the number of functional proteomes and proteins,improve the taste of CWECM solutions,and improve the therapeutic efficacy of CWECM.

Surviving winter on the Qinghai-Xizang Plateau:Extensive reversible protein phosphorylation plays a dominant role in regulating hypometabolism in hibernating Nanorana parkeri

Changes in protein abundance and reversible protein phosphorylation(RPP)play important roles in regulating hypometabolism but have never been documented in overwintering frogs at high altitudes.To test the hypothesis that protein abundance and phosphorylation change in response to winter hibernation,we conducted a comprehensive and quantitative proteomic and phosphoproteomic analysis of the liver of the Xizang plateau frog,Nanorana parkeri,living on the Qinghai-Xizang Plateau.In total,5170 proteins and 5695 phosphorylation sites in 1938 proteins were quantified.Based on proteomic analysis,674 differentially expressed proteins(438 up-regulated,236 down-regulated)were screened in hibernating N.parkeri versus summer individuals.Functional enrichment analysis revealed that higher expressed proteins in winter were significantly enriched in immune-related signaling pathways,whereas lower expressed proteins were mainly involved in metabolic processes.A total of 4251 modified sites(4147 up-regulated,104 down-regulated)belonging to 1638 phosphoproteins(1555 up-regulated,83 down-regulated)were significantly changed in the liver.During hibernation,RPP regulated a diverse array of proteins involved in multiple functions,including metabolic enzymatic activity,ion transport,protein turnover,signal transduction,and alternative splicing.These changes contribute to enhancing protection,suppressing energy-consuming processes,and inducing metabolic depression.Moreover,the activities of phosphofructokinase,glutamate dehydrogenase,and ATPase were all significantly lower in winter compared to summer.In conclusion,our results support the hypothesis and demonstrate the importance of RPP as a regulatory mechanism when animals transition into a hypometabolic state.

Neuroprotective effects of acteoside in a glaucoma mouse model by targeting Serta domain-containing protein 4

AIM:To explore the therapeutic effect and main molecular mechanisms of acteoside in a glaucoma model in DBA/2J mice.METHODS:Proteomics was used to compare the differentially expressed proteins of C57 and DBA/2J mice.After acteoside administration in DBA/2J mice,anterior segment observation,intraocular pressure(IOP)monitoring,electrophysiology examination,and hematoxylin and eosin staining were used to analyze any potential effects.Immunohistochemistry(IHC)assays were used to verify the proteomics results.Furthermore,retinal ganglion cell 5(RGC5)cell proliferation was assessed with cell counting kit-8(CCK-8)assays.Serta domain-containing protein 4(Sertad4)mRNA and protein expression levels were measured by qRT-PCR and Western blot analysis,respectively.RESULTS:Proteomics analysis suggested that Sertad4 was the most significantly differentially expressed protein.Compared with the saline group,the acteoside treatment group showed decreased IOP,improved N1-P1 wave amplitudes,thicker retina,and larger numbers of cells in the ganglion cell layer(GCL).The IHC results showed that Sertad4 expression levels in DBA/2J mice treated with acteoside were significantly lower than in the saline group.Acteoside treatment could improve RGC5 cell survival and reduce the Sertad4 mRNA and protein expression levels after glutamate injury.CONCLUSION:Sertad4 is differentially expressed in DBA/2J mice.Acteoside can protect RGCs from damage,possibly through the downregulation of Sertad4,and has a potential use in glaucoma treatment.

Changes in milk fat globule membrane proteins along lactation stage of Laoshan dairy goat

The milk fat globule membrane(MFGM)is a complex structure with numerous functions,and its composition is affected by many factors.There have been few systematic investigations on goat MFGM proteome profiling during lactation.Individual milk samples from 15 healthy dairy goats were obtained at six lactation time points for investigation of the MFGM proteome using both data-independent acquisition(DIA)and data-dependent acquisition(DDA)proteomics techniques combined with multivariate statistical analysis.Using the DIA method,890 variably abundant MFGM proteins were discovered throughout the lactation cycle.From 1 to 240 d,butyrophilin subfamily 1 member A1,lipoprotein lipase,perilipin-2,and adipose triglyceride lipase were upregulated,while APOE,complement C3,clusterin,and IgG were downregulated.Furthermore,from 1 to 90 d,annexin A1,annexin A2,and antithrombin-ll were downregulated,then upregulated by d 240.Albumin had a high degree of connectedness,indicating that it was a key protein,according to protein-protein interaction research.Overall,our findings gave new insights into the biological features of MFGM protein in goat milk throughout lactation,which may aid in the creation of specialized MFGM products and infant formula.

Dynamic changes of root proteome reveal diverse responsive proteins in maize subjected to cadmium stress

Toxic symptoms and tolerance mechanisms of heavy metal in maize are well documented. However, limited information is available regarding the changes in the proteome of maize seedling roots in response to cadmium(Cd) stress. Here, we employed an i TRAQ-based quantitative proteomic approach to characterize the dynamic alterations in the root proteome during early developmental in maize seedling. We conducted our proteomic experiments in three-day seedling subjected to Cd stress, using roots in four time points. We identified a total of 733, 307, 499, and 576 differentially abundant proteins after 12, 24, 48, or 72 h of treatment, respectively. These proteins displayed different functions, such as ribosomal synthesis, reactive oxygen species homeostasis, cell wall organization, cellular metabolism, and carbohydrate and energy metabolism. Of the 166 and 177 proteins with higher and lower abundance identified in at least two time points, 14 were common for three time points. We selected nine proteins to verify their expression using quantitative real-time PCR. Proteins involved in the ribosome pathway were especially responsive to Cd stress. Functional characterization of the proteins and the pathways identified in this study could help our understanding of the complicated molecular mechanism involved in Cd stress responses and create a list of candidate gene responsible for Cd tolerance in maize seeding roots.