Comparative proteomics analysis reveals the domesticated Lepista sordida primordium differentiation regulation mechanism and the subsequent different development patterns in the pileus and stipe

The wild Lepista sordida is a kind of precious and rare edible fungus.An excellent strain of it by artificial domestication was obtained,which was high-yield and high in iron content.In this study,high-throughput comparative proteomics was used to reveal the regulatory mechanism of its primordium differentiation in the early fruiting body formation.The mycelium before the primordium differentiation mainly expressed high levels of mitochondrial functional proteins and carbon dioxide concentration regulatory proteins.In young mushrooms,the highly expressed proteins were mainly involved in cell component generation,cell proliferation,nitrogen compound metabolism,nucleotide metabolism,glutathione metabolism,and purine metabolism.The differential regulation patterns of pileus and stipe growth to maturity were also revealed.The highly expressed proteins related to transcription,RNA splicing,the production of various organelles,DNA conformational change,nucleosome organization,protein processing,maturation and transport,and cell detoxification regulated the pileus development and maturity.The proteins related to carbohydrate and energy metabolism,large amounts of obsolete cytoplasmic parts,nutrient deprivation,and external stimuli regulated the stipe development and maturity.Multiple CAZymes regulated nutrient absorption,morphogenesis,spore production,stress response,and other life activities at different growth and development stages.

Comparative proteomics analysis of tea leaves exposed to subzero temperature:Molecular mechanism of freeze injury

Tea freeze injury is one of the most severe agro-meteorological disasters,which leads to sizable losses of tea production in China.The freezing resistant ability of overwintering tea trees becomes weaker and weaker from early-spring to late-spring.If it decreases to critical temperature of-2℃or lower in the stage with one or two leaves,tea trees suffer from freeze injury and the yield or quality of spring tea production could decrease greatly.Although measurements have been taken to prevent such damage,the physiological and biochemical mechanism of how tea(Camellia Sinensis)plant response to freeze injury is still to be elucidated.A comparative proteomics analysis was made on tea leaves at the two-leaf stage.The differential image analysis showed 46 spots with density changes(29 spots increased and 17 spots decreased;p<0.01)in the freeze injury group compared with the control group.Thirty eight differential protein spots(p<0.01)with good resolution and relatively high abundance in MS were subjected to further protein identification.Among them,all 17 up-regulated spots were collected whereas only six of the down-regulated spots were selected.These differentially expressed proteins including heat shock protein 70,oxygen-evolving enhancer protein,adenosine triphosphate synthase,S-adenosylmethionine synthetase and some enzymes involved in carbohydrate metabolism,were shown responsive to freeze injury.The results would greatly increase the comprehension of the molecular mechanism for freeze injury and provide a better decision making for freeze protection and control.

Comparative Proteomic Analysis in Left Ventricular Remodeling following Myocardial Infarction in Rats

Objective Left ventricular remodeling （LVR） following myocardial infarction （MI） is a key pathophysiological process in which MI develops into heart failure. The exact mechanism of LVR remains unclear. We performed differential proteomic analysis on the myocardia of rats with LVR after MI, to explore the mechanism of ventricular remodeling after MI. Methods In the LVR group （n=12）, after the anterior descending coronary artery was ligated, the rats were fed for four weeks before the LVR models were established. Rats in the sham-operated group （n=11） underwent thread-drawing without ligation. The hemodynamic parameters, pathological findings, and proteomics were compared between the two groups. Results In the LVR group, the left ventricular end-diastolic pressure increased, the maximal left ventricular pressure increase/decrease ratio decreased significantly, and the left ventricular systolic pressure decreased. H-E staining and Masson staining of cardiac muscle tissues of the LVR group showed myocytolysis, disarray, and collagen proliferation. Twenty-one differentially expressed proteins were detected by proteomic analysis. We validated two proteins using western blot analysis. The differentially expressed proteins could be divided into six categories： energy metabolism-related proteins, cytoskeletal proteins, protein synthesis-related proteins, channel proteins, anti-oxidation- related proteins, and immune-related proteins. Conclusion These differentially expressed proteins might play key roles in LVR following M

Comparative proteomic analysis of plasma proteins in patients with age-related macular degeneration

AIM:To find the significant altered proteins in agerelated macular degeneration(AMD)patients as potential biomarkers of AMD.METHODS:A comparative analysis of the protein pattern of AMD patients versus healthy controls was performed by means of proteomic analysis using twodimensional gel electrophoresis followed by protein identification with MALDI TOF/TOF mass spectrometry.RESULTS:We identified 28 proteins that were significantly altered with clinical relevance in AMD patients.These proteins were involved in a wide range of biological functions including immune responses,growth cytokines,cell fate determination,wound healing,metabolism,and anti-oxidance.CONCLUSION:These results demonstrate the capacity of proteomic analysis of AMD patient plasma.In addition to the utility of this approach for biomarker discovery,identification of alterations in endogenous proteins in the plasma of AMD patient could improve our understanding of the disease pathogenesis.

Comparative Proteomic Analysis of the Fiber Elongating Process in Cotton

A comparative proteomic analysis was performed to explore the mechanism of cell elongation in developing cotton fibers.The temporal changes of global proteomes at five representative

Comparative proteomic analysis of hippocampal proteins from chronic stressed rats

Chronic stress can induce hippocampus injury such as neuron loss and dendrite atrophy,but its mechanism and molecular basis remain unclear up to now.To understand the molecular mechanism on protein level and find the crucial proteins which correlated with chronic

Comparative proteomic analysis of renal tubular epithelial cell injury caused by oxalic acid and calcium oxalate monohydrate

Objective To analyze and identify the differentially expressed proteins in human renal tubular epithelial ceils ( HK-2) after injury caused by oxalic acid and calcium oxalate monohydrate ( COM ) crystal,and to explore the potential role of renal tubular cell injury in kidney stone formation. Methods Normal HK-2 cells

Proteomic analysis of seminal plasma from asthenozoospermia patients reveals proteins that affect oxidative stress responses and semen quality

Asthenozoospermia （AS） is a common cause of human male infertility. In one study, more than 80% of the samples from infertile men had reduced sperm motility. Seminal plasma is a mixture of secretions from the testis, epididymis and several male accessory glands, including the prostate, seminal vesicles and Cowper＇s gland. Studies have shown that seminal plasma contains proteins that are important for sperm motility. To further explore the pathophysiological character of AS, we separated the seminal plasma proteins from AS patients and healthy donors using sodium dodecyl sulfate polyacrylamide gel electrophoresis and in-gel digestion, and then subjected the proteins to liquid chromatography-mass spectrometry （LC-MS/MS） analysis. A total of 741 proteins were identified in the seminal plasma, with a false discovery rate of 3.3%. Using spectral counting, we found that 45 proteins were threefold upregulated and 56 proteins were threefold downregulated in the AS group when compared with the control. Most of these proteins originated from the epididymis and prostate. This study identified a rich source of biomarker candidates for male infertility and indicates that functional abnormalities of the epididymis and prostate can contribute to AS. We identified D J-1--a protein that has been shown elsewhere to be involved in the control of oxidative stress （OS）-as a downregulated protein in AS seminal plasma. The levels of D J-1 in AS seminal plasma were about half of those in the control samples. In addition, the levels of reactive oxygen species were 3.3-fold higher in the AS samples than in the controls. Taken together, these data suggest that downregulation of DJ-1 is involved in OS in semen, and therefore affects the quality of the semen.

Proteomic-based evidence for adult neurogenesis in birds and mammals as indicated from cerebrospinal fluid

Adult neurogenesis is the life-long process of neural stem cell proliferation,differentiation into neurons,migration,and incorporation into the existing neuronal circuits.After decades of research,it is now widely accepted that mammals and birds retain the capacity to regenerate neurons even after their subadult ontogeny.Cerebrospinal fluid participates in the regulation of the neurogenic niches of the vertebrate brain through signaling pathways not fully elucidated.Proteomic studies of cerebrospinal fluid have the potential to allow the in-depth characterization of its molecular composition.Comparative studies help to delineate those pathways that are universally critical for the regulation of neurogenesis in adulthood.In this review,we performed literature-based data mining in studies using liquid chromatography-tandem mass spectroscopy that analyzed cerebrospinal fluid samples from healthy adult humans(Homo sapiens);mice(Mus musculus);sheep(Ovis aries);chickens(Gallus gallus);and two parrot species,the budgerigar(Melopsittacus undulatus)and cockatiel(Nymphicus hollandicus).We identified up to 911 proteins represented in cerebrospinal fluid,involved in various pathways regulating adult neurogenesis.However,only 196 proteins were common across humans,mice,and birds.Pathway components involved in nervous system development,cell migration,and axonal guidance were commonly evident in all species investigated so far.Extensive bioinformatic analysis revealed that the universally over-represented pathways involved L1 cell adhesion molecule protein interactions,cell-adhesion molecules,signals regulating extracellular matrix remodeling,regulation of insulin growth factor signaling,axonal guidance,programmed cell death,immune signaling,and post-translational modifications.Most of the reported proteins are part of extracellular vesicles enriched in cerebrospinal fluid.However,the information presently available is still highly fragmentary,and far more questions persist than are answered.Technological advances will allow cerebrospinal fluid comparative proteomic research to delve into the fundamental processes of adult neurogenesis and eventually translate this research into any regenerative interventions.

Easy-to-use Method to Display Arabidopsis Rubisco Interacting Proteins

Affinity-mediated protein separation is an integral part of proteomics, the most outstanding of which is immunoproteomics. However, in the immunoprecipitate system overwhelming Ab and Ag conceal Ag interacting proteins as the research targets, which is the rate-limiting step in the progress of comparative proteomic analyses. We presented a convenient and accurate method to tackle this problem. 1 mol/L NaCl elution buffer was applied to the complex Rubisco immunoprecipitate of Arabidopsis, the weakest force involved in the system was selectively broken up, resulting in the enrichment of Rubisco interacting proteins accessible for further comparative protein gel profile. The easy-to-use method sheds light on a narrow-down strategy supplement for comparative immunoproteomics.

Antimicrobial activity and mode of action of terpene linalyl anthranilate against carbapenemase-producing Klebsiella pneumoniae

Mining of plant-derived antimicrobials is the major focus at current to counter antibiotic resistance. This study was conducted to characterize the antimicrobial activity and mode of action of linalyl anthranilate(LNA) against carbapenemase-producing Klebsiella pneumoniae(KPC-KP). LNA alone exhibited bactericidal activity at 2.5%(V/V), and in combination with meropenem(MPM) at 1.25%(V/V). Comparative proteomic analysis showed a significant reduction in the number of cytoplasmic and membrane proteins,indicating membrane damage in LNA-treated KPC-KP cells. Up-regulation of oxidative stress regulator proteins and down-regulation of oxidative stress-sensitive proteins indicated oxidative stress. Zeta potential measurement and outer membrane permeability assay revealed that LNA increases both bacterial surface charge and membrane permeability. Ethidium bromide influx/efflux assay showed increased uptake of ethidium bromide in LNA-treated cells, inferring membrane damage. Furthermore, intracellular leakage of nucleic acid and proteins was detected upon LNA treatment. Scanning and transmission electron microscopies again revealed the breakage of bacterial membrane and loss of intracellular materials. LNA was found to induce oxidative stress by generating reactive oxygen species(ROS) that initiate lipid peroxidation and damage the bacterial membrane. In conclusion, LNA generates ROS, initiates lipid peroxidation, and damages the bacterial membrane, resulting in intracellular leakage and eventually killing the KPC-KP cells.

Ascorbate peroxidase 1 confers resistance to southern corn leaf blight in maize

Southern corn leaf blight (SCLB), caused by Bipolarismaydis, is one of the most devastatingdiseases affecting maize production. However,only one SLCB resistance gene, conferring partialresistance, is currently known, underscoring theimportance of isolating new SCLB resistancerelatedgenes. Here, we performed a comparativeproteomic analysis and identified 258 proteinsshowing differential abundance during the maizeresponse to B. maydis. These proteins included anascorbate peroxidase (Zea mays ascorbate peroxidase1 (ZmAPX1)) encoded by a gene locatedwithin the mapping interval of a previously identifiedquantitative trait locus associated with SCLBresistance. ZmAPX1 overexpression resulted inlower H_(2)O_(2) accumulation and enhanced resistanceagainst B. maydis. Jasmonic acid (JA)contents and transcript levels for JA biosynthesisand responsive genes increased in ZmAPX1-overexpressing plants infected with B. maydis,whereas Zmapx1 mutants showed the oppositeeffects. We further determined that low levels of H_(2)O_(2) are accompanied by an accumulation of JAthat enhances SCLB resistance. These resultsdemonstrate that ZmAPX1 positively regulatesSCLB resistance by decreasing H_(2)O_(2) accumulationand activating the JA-mediated defensesignaling pathway. This study identified ZmAPX1as a potentially useful gene for increasing SCLBresistance. Furthermore, the generated datamay be relevant for clarifying the functions ofplant APXs.

Surveying the Oligomeric State of Arabidopsis thaliana Chloroplasts

Blue native-PAGE （BN-PAGE） resolves protein complexes in their native state. When combined with immu- noblotting, it can be used to identify the presence of high molecular weight complexes at high resolution for any protein, given a suitable antibody. To identify proteins in high molecular weight complexes on a large scale and to bypass the requirement for specific antibodies, we applied a tandem mass spectrometry （MS/MS） approach to BN-PAGE-resolved chloroplasts. Fractionation of the gel into six bands allowed iden- tification and label-free quantification of 1000 chloroplast proteins with native molecular weight separation. Significantly, this approach achieves a depth of identification comparable with traditional shotgun proteo- mic analyses of chloroplasts, indicating much of the known chloroplast proteome is amenable to MS/MS identification under our fractionation scheme. By limiting the number of fractionation bands to six, we facil- itate scaled-up comparative analyses, as we demonstrate with the reticulata chloroplast mutant displaying a reticulated leaf phenotype. Our comparative proteomics approach identified a candidate interacting protein of RETICULATA as well as effects on lipid remodeling proteins, amino acid metabolic enzymes, and plastid division machinery. We additionally highlight selected proteins from each sub-compartment of the chloroplast that provide novel insight on known or hypothesized protein complexes to further illus- trate the utility of this approach. Our results demonstrate the high sensitivity and reproducibility of this technique, which is anticipated to be widely adaptable to other sub-cellular compartments.