Evidence showed that N6-methyladenosine(m^(6)A)modification plays a pivotal role in influencing RNA fate and is strongly associated with cell growth and developmental processes in many species.However,no information r...Evidence showed that N6-methyladenosine(m^(6)A)modification plays a pivotal role in influencing RNA fate and is strongly associated with cell growth and developmental processes in many species.However,no information regarding m^(6)A modification in Eimeria tenella is currently available.In the present study,we surveyed the transcriptome-wide prevalence of m^(6)A in sporulated oocysts and unsporulated oocysts of E.tenella.Methylated RNA immunoprecipitation sequencing(MeRIP-seq)analysis showed that m^(6)A modification was most abundant in the coding sequences,followed by stop codon.There were 3,903 hypermethylated and 3,178 hypomethylated mRNAs in sporulated oocysts compared with unsporulated oocysts.Further joint analysis suggested that m^(6)A modification of the majority of genes was positively correlated with mRNA expression.The mRNA relative expression and m^(6)A level of the selected genes were confirmed by quantitative reverse transcription PCR(RT-qPCR)and MeRIP-qPCR.GO and KEGG analysis indicated that differentially m^(6)A methylated genes(DMMGs)with significant differences in mRNA expression were closely related to processes such as regulation of gene expression,epigenetic,microtubule,autophagy-other and TOR signaling.Moreover,a total of 96 DMMGs without significant differences in mRNA expression showed significant differences at protein level.GO and pathway enrichment analysis of the 96 genes showed that RNA methylation may be involved in cell biosynthesis and metabolism of E.tenella.We firstly present a map of RNA m^(6)A modification in E.tenella,which provides significant insights into developmental biology of E.tenella.展开更多
Previous studies have revealed that ammonia nitrogen has several adverse effects on clam Ruditapes philippinarum.However,knowledge is lacking regarding the related proteins involved in the toxicological responses,whic...Previous studies have revealed that ammonia nitrogen has several adverse effects on clam Ruditapes philippinarum.However,knowledge is lacking regarding the related proteins involved in the toxicological responses,which is vital to elucidate the underlying mechanism of ammonia nitrogen.In this study,clams R.philippinarum were exposed to ammonia nitrogen for 21 d at two environmentally relevant concentrations.The tandem mass tags approach(TMT)was applied to assay the differentially expressed proteins(DEPs)in clam gill tissues on the 3 rd and 21 st day.Finally,a total of 7263 proteins were identified.Bioinformatics analyses revealed that clam protein profiles changed in dose-and time dependent manner after ammonia nitrogen exposure.We inferred that the clams may face heavy challenges after ammonia exposure,such as unbalanced gender ratio,lysosomal disease,energy lack,neurological disorders,altered glutamine metabolism,increased lipid synthesis,and impaired immunity.Variation profiles of enzyme activities of glutaminase and glutamine synthase provided direct evidence to verify the related inference from proteome data.Most of the inferred toxic effects merit further study.This study identified important proteins related to ammonia nitrogen toxicity in the clam and indicated the severe stress of marine ammonia pollution on the healthy development of mollusc aquaculture.展开更多
Peroxisomes compartmentalize a dynamic suite of biochemical reactions and play a central role in plant metabolism, such as the degradation of hydrogen peroxide, metabolism of fatty acids, photorespiration, and the bio...Peroxisomes compartmentalize a dynamic suite of biochemical reactions and play a central role in plant metabolism, such as the degradation of hydrogen peroxide, metabolism of fatty acids, photorespiration, and the biosyn- thesis of plant hormones. Plant peroxisomes have been traditionally classified into three major subtypes, and in-depth mass spectrometry （MS）-based proteomics has been per- formed to explore the proteome of the two major subtypes present in green leaves and etiolated seedlings. Here, we carried out a comprehensive proteome analysis of perox- isomes from Arabidopsis leaves given a 48-h dark treatment. Our goal was to determine the proteome of the third major subtype of plant peroxisomes from senescent leaves, and further catalog the plant peroxisomal proteome. We identified a total of 111 peroxisomal proteins and verified the peroxisomal localization for six new proteins with potential roles in fatty acid metabolism and stress response by in vivo targeting analysis. Metabolic pathways compartmentalized in the three major subtypes of peroxisomes were also compared, which revealed a higher number of proteins involved in the detoxification of reactive oxygen species in peroxisomes from senescent leaves. Our study takes an important step towards mapping the full function of plant peroxisomes.展开更多
Phosphorus(P) deficiency limits the growth,development,and productivity of rice.To better understand the underlying mechanisms in P-deficiency tolerance and the role of Pup1 QTL in enhancing P use efficiency(PUE) for ...Phosphorus(P) deficiency limits the growth,development,and productivity of rice.To better understand the underlying mechanisms in P-deficiency tolerance and the role of Pup1 QTL in enhancing P use efficiency(PUE) for the development of P-efficient rice cultivars,a pair of contrasting rice genotypes(Pusa-44 and NIL-23) was applied to investigate the morpho-physio-biochemical and proteomic variation under P-starvation stress.The rice genotypes were grown hydroponically in a PusaRich medium with adequate P(16 mg/kg,+P) or without P(0 mg/kg,-P) for 30 d.P-starvation manifested a significant reductions in root and shoot biomass,shoot length,leaf area,total chlorophyll,and P,nitrogen and starch contents,as well as protein kinase activity.The stress increased root-to-shoot biomass ratio,root length,sucrose content,and acid phosphatase activity,particularly in the P-tolerant genotype(NIL-23).Comparative proteome analysis revealed several P metabolism-associated proteins(including OsCDPKs,OsMAPKs,OsCPKs,OsLecRK2,and OsSAPks) to be expressed in the shoot of NIL-23,indicating that multiple protein kinases were involved in P-starvation/deficiency tolerance.Moreover,the up-regulated expression of OsrbcL,OsABCG32,OsSUS5,OsPoll-like B,and ClpC2 proteins in the shoot,and OsACA9,OsACA8,OsSPS2F,OsPP2C15,and OsBiP3 in the root of NIL-23,indicated their role in P-starvation stress control through the Pup1 QTL. Thus,our findings indicated that-P stress-responsive proteins,in conjunction with morpho-physio-biochemical modulations,improved PUE and made NIL-23 a P-deficiency tolerant genotype due to the introgression of the Pup1 QTL in the Pusa-44 background.展开更多
The environmental characteristics of hypothermia and hypoxia exert great selective pressure on the energy metabolism of high-altitude animals,especially the ectotherms.Current research on energy-limited adaptation of ...The environmental characteristics of hypothermia and hypoxia exert great selective pressure on the energy metabolism of high-altitude animals,especially the ectotherms.Current research on energy-limited adaptation of high-altitude ectotherms has focused on energy expenditures.However,the mechanisms of increasing energy intake in high-altitude ectotherms have been studied rarely.In order to investigate the adaptation mechanism of the small intestine,the key part of energy acquisition for animals,to energy limitation at high altitude in ectotherms,the gut proteins of Phrynocephalus vlangalii from high-and low-altitude populations were compared using label free proteomics.GO enrichment and KEGG pathway analysis showed that proteins associated with energy intake,such as those involved in oxidation-reduction processes,glutathione metabolism,oxidoreductase activity,cofactor binding,catalytic activity and metabolic pathways,were significantly up-regulated in high-altitude populations;while proteins associated with energy expenditure,such as immune responses and processes,membrane attack complexes,natural killer pathway and other immune-related processes,were significantly down-regulated in expression.展开更多
BACKGROUND The function of prohibitin 1(Phb1)during liver regeneration(LR)remains relatively unexplored.Our previous research identified downregulation of Phb1 in rat liver mitochondria 24 h after 70%partial hepatecto...BACKGROUND The function of prohibitin 1(Phb1)during liver regeneration(LR)remains relatively unexplored.Our previous research identified downregulation of Phb1 in rat liver mitochondria 24 h after 70%partial hepatectomy(PHx),as determined by subcellular proteomic analysis.AIM To investigate the potential role of Phb1 during LR.METHODS We examined changes in Phb1 mRNA and protein levels,subcellular distribution,and abundance in rat liver during LR following 70%PHx.We also evaluated mitochondrial changes and apoptosis using electron microscopy and flow cytometry.RNA-interference-mediated knockdown of Phb1(PHBi)was performed in BRL-3A cells.RESULTS Compared with sham-operation control groups,Phb1 mRNA and protein levels in 70%PHx test groups were downregulated at 24 h,then upregulated at 72 and 168 h.Phb1 was mainly located in mitochondria,showed a reduced abundance at 24 h,significantly increased at 72 h,and almost recovered to normal at 168 h.Phb1 was also present in nuclei,with continuous increase in abundance observed 72 and 168 h after 70%PHx.The altered ultrastructure and reduced mass of mitochondria during LR had almost completely recovered to normal at 168 h.PHBi in BRL-3A cells resulted in increased S-phase entry,a higher number of apoptotic cells,and disruption of mitochondrial membrane potential.CONCLUSION Phb1 may contribute to maintaining mitochondrial stability and could play a role in regulating cell proliferation and apoptosis of rat liver cells during LR.展开更多
Proteomics was used to reveal the differential protein expression profiles of acute responses to copper sulfate exposure in larvae of Artemia sinica.Fourteen differentially displayed protein spots were detected and se...Proteomics was used to reveal the differential protein expression profiles of acute responses to copper sulfate exposure in larvae of Artemia sinica.Fourteen differentially displayed protein spots were detected and seven of them were identified.Three spots were up-expressed and identified:actin, heat shock protein 70,and chaperone subunit 1;three down-regulated proteins were identified:arginine kinase,elongation factor-2,and glycine-rich protein;and a newly expressed protein was identified as peroxiredoxin.The study indicates the involvement of all the differentially expressed proteins in the early responses of protein expression,and in the survival of A.sinica in the presence of copper and other heavy metals;the findings improve understanding of the organism’s adaptive responses and resistance.展开更多
BACKGROUND: Early diagnosis of liver metastasis of colorectal carcinoma is very important for the appropriate treatment of such patients. However, there has been no effective approach available for clinical applicatio...BACKGROUND: Early diagnosis of liver metastasis of colorectal carcinoma is very important for the appropriate treatment of such patients. However, there has been no effective approach available for clinical application. The present study aimed to investigate the differential expression of proteins in patients with liver metastasis of colorectal carcinomas using proteomic analysis and evaluate its potentiality in clinical diagnosis. METHODS: Fluorescence two-dimensional differential in-gel electrophoresis (2-D DIGE) was used to analyze and compare the protein expression between normal mucosa, the primary focus, and liver metastases. Proteomic analysis was made to identify the differentially expressed proteins. Immunohistological staining was used to confirm the expression of differentially expressed proteins in colorectal carcinomas and areas of liver metastasis. RESULTS: A 1.5-fold difference was found with 46 differentially expressed proteins. In 20 differentially expressed proteins, 3 were down-regulated and 17 up-regulated in liver metastases. Proteomic analysis showed that the S-adenosylmethionine transgelin variant was down-regulated in liver metastasis tissues. Zinc finger protein 64 homolog (Zfp64), guanine nucleotide exchange factor 4 (GEF4), human arginase, glutathione S-transferases (GSTs) A3, and tumor necrosis factor a (TNF-alpha)-induced protein 9 were up-regulated in liver metastasis tissues. Immunohistochemical staining confirmed that human arginase expression was higher in liver metastases than in the primary focus. CONCLUSIONS: There was a significant difference in protein expression between the primary focus of colorectal carcinoma and liver metastases. The differentially regulated proteins were closely related to liver metastasis of colorectal carcinoma. Elevated human arginase may be an important molecular marker for liver metastasis from colorectal carcinoma. (Hepatobiliary Pancreat Dis Jut 2010; 9: 149-153)展开更多
Engineered Corynebacterium glutamicum was constructed for L-ornithine production by disrupting genes of argF and proB to prevent the flux away from L-ornithine.Effect of the inactivation of 2-oxoglutarate de-hydrogena...Engineered Corynebacterium glutamicum was constructed for L-ornithine production by disrupting genes of argF and proB to prevent the flux away from L-ornithine.Effect of the inactivation of 2-oxoglutarate de-hydrogenase complex(ODHC) on L-ornithine production was also investigated.It was found that the inactivation of ODHC by knockout of the kgd gene enhanced L-ornithine production.The engineered C.glutamicum ATCC13032(ΔargFΔproBΔkgd) produced L-ornithine up to 4.78 g·L-1 from 0.24 g·L-1 of the wild-type strain.In order to understand the mechanism of L-ornithine production in C.glutamicum ATCC13032(ΔargFΔproBΔkgd) and find out new strategies for further enhancing L-ornithine production,the comparative proteome between the wild-type and the engineered strain was analyzed.L-Ornithine overproduction in the engineered strain was related to the up-regulation of the expression levels of enzymes involved in L-ornithine biosynthesis pathway and down-regulation of the expression levels of proteins involved in pentose phosphate pathway.The overexpression of genes in the upstream pathway of glutamate to increase the availability of endogenous glutamate may further in-crease ornithine production in the engineered C.glutamicum and the ornithine synthesis enzymes(ArgCJBD) may not be the limiting enzymes in the engineered C.glutamicum.展开更多
Viruses of thermophiles are of great interest due to their roles in gene transfer, global geochemical cycle and evolution of life on earth. However, the thermophilic bacteriophages have not been studied extensively. I...Viruses of thermophiles are of great interest due to their roles in gene transfer, global geochemical cycle and evolution of life on earth. However, the thermophilic bacteriophages have not been studied extensively. In this investigation, a typical bacteriophage BV1 was obtained from a thermophilic bacterium Geobacillus sp. 6k512, which was isolated from an inshore hot spring in Xiamen of China. The BV1 contained a double-stranded linear DNA of 35 055 bp, which encodes 54 open reading frames （ORFs）. Interestingly, eight of the 54 BV1 ORFs shared sequence similarities to genes from human disease-relevant bacteria. Seven proteins of the purified BV1 virions were identified by proteomic analysis. Determination of BV1 functional genomics would facilitate the better understanding of the mechanism for virus-thermophile interaction.展开更多
Our previous study has confirmed that astrocytes overexpressing neurogenic differentiation factor 1(NEUROD1)in the spinal cord can be reprogrammed into neurons under in vivo conditions.However,whether they can also be...Our previous study has confirmed that astrocytes overexpressing neurogenic differentiation factor 1(NEUROD1)in the spinal cord can be reprogrammed into neurons under in vivo conditions.However,whether they can also be reprogrammed into neurons under in vitro conditions remains unclear,and the mechanisms of programmed conversion from astrocytes to neurons have not yet been clarified.In the present study,we prepared reactive astrocytes from newborn rat spinal cord astrocytes using the scratch method and infected them with lentivirus carrying NEUROD1.The results showed that NEUROD1 overexpression reprogrammed the cultured reactive astrocytes into neurons in vitro with an efficiency of 13.4%.Using proteomic and bioinformatic analyses,1952 proteins were identified,of which 92 were differentially expressed.Among these proteins,11 were identified as candidate proteins in the process of reprogramming based on their biological functions and fold-changes in the bioinformatic analysis.Furthermore,western blot assay revealed that casein kinase II subunit alpha(CSNK2A2)and pinin(PNN)expression in NEUROD1-overexpressing reactive astrocytes was significantly increased,suggesting that NEUROD1 can directly reprogram spinal cord-derived reactive astrocytes into neurons in vitro,and that the NEUROD1-CSNK2A2-PNN pathway is involved in this process.This study was approved by the Animal Ethics Committee of Fujian Medical University,China(approval No.2016-05)on April 18,2016.展开更多
AIM:To analyze the retinal proteomes with and without conbercept treatments in mice with oxygen-induced retinopathy(OIR)and identify proteins involved in the molecular mechanisms mediated by conbercept.METHODS:OIR was...AIM:To analyze the retinal proteomes with and without conbercept treatments in mice with oxygen-induced retinopathy(OIR)and identify proteins involved in the molecular mechanisms mediated by conbercept.METHODS:OIR was induced in fifty-six C57 BL/6 J mouse pups and randomly divided into four groups.Group 1:Normal17(n=7),mice without OIR and treated with normal air.Group 2:OIR12/EXP1(n=14),mice received 75%oxygen from postnatal day(P)7 to 12.Group 3:OIR17/Control(n=14),mice received 75%oxygen from P7 to P12 and then normal air to P17.Group 4:Lang17/EXP2(n=21),mice received 75%oxygen from P7 to P12 with intravitreal injection of 1μL conbercept at the concentration of 10 mg/m L at P12,and then normal air from P12 to P17.Liquid ChromatographyMass Spectrometry(LC-MS)/MS data were reviewed to find proteins that were up-regulated after the conbercept treatment.Gene ontology(GO)analysis was performed of conbercept-mediated changes in proteins involved in single-organism processes,biological regulation,cellular processes,immune responses,metabolic processes,locomotion and multiple-organism processes.RESULTS:Conbercept induced a reversal of hypoxiainducible factor 1 signaling pathway as revealed by the Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis and also induced down-regulation of proteins involved in blood coagulation and fibrin clot formation as demonstrated by the Database for Annotation,Visualization and Integrated Discovery(DAVID)and the stimulation of interferon genes studies.These appear to be risk factors of retinal fibrosis.Additional conbercept-specific fibrosis risk factors were also identified and may serve as therapeutic targets for fibrosis.CONCLUSION:Our studies reveal that many novel proteins are differentially regulated by conbercept.The new insights may warrant a valuable resource for conbercept treatment.展开更多
Background:Guben Zhike decoction(GBZKD)is derived from the experience of Professor Enxiang Chao,an esteemed master of Chinese medicine,while treating chronic obstructive pulmonary disease(COPD).GBZKD reinforces the he...Background:Guben Zhike decoction(GBZKD)is derived from the experience of Professor Enxiang Chao,an esteemed master of Chinese medicine,while treating chronic obstructive pulmonary disease(COPD).GBZKD reinforces the healthy qi and consolidates defensive qi.This study explored the efficacy and potential mechanism of action of GBZKD in a COPD mouse model using proteomics.Methods:A COPD mouse model was established through cigarette smoke exposure and intranasal lipopolysaccharide administration.The model was verified through lung function test and lung histopathological observation.Label-free quantitative proteomics was used to detect the lung tissue proteins of mice from the GBZKD,COPD,and control groups.Results:GBZKD markedly improved the lung function and associated pathological conditions in the COPD mouse model.Proteomic analysis identified 4316 proteins,of which 3696 were quantitative proteins.We highlighted 287 and 184 proteins with significant regulatory roles in the lung tissues of COPD mice and GBZKD-treated mice,respectively.These proteins participated in multiple functions,including complement/coagulation cascade,immune response,and metabolic pathways.Conclusion:GBZKD exhibits multitarget and multipathway therapeutic effects in a COPD mouse model.展开更多
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
The composition of serum is extremely complex,which complicates the discovery of new pharmacodynamic biomarkers via serum proteome for disease prediction and diagnosis.Recently,nanoparticles have been reported to effi...The composition of serum is extremely complex,which complicates the discovery of new pharmacodynamic biomarkers via serum proteome for disease prediction and diagnosis.Recently,nanoparticles have been reported to efficiently reduce the proportion of high-abundance proteins and enrich lowabundance proteins in serum.Here,we synthesized a silica-coated iron oxide nanoparticle and developed a highly efficient and reproducible protein corona(PC)-based proteomic analysis strategy to improve the range of serum proteomic analysis.We identified 1,070 proteins with a median coefficient of variation of 12.56%using PC-based proteomic analysis,which was twice the number of proteins identified by direct digestion.There were also more biological processes enriched with these proteins.We applied this strategy to identify more pharmacodynamic biomarkers on collagen-induced arthritis(CIA)rat model treated with methotrexate(MTX).The bioinformatic results indicated that 485 differentially expressed proteins(DEPs)were found in CIA rats,of which 323 DEPs recovered to near normal levels after treatment with MTX.This strategy can not only help enhance our understanding of the mechanisms of disease and drug action through serum proteomics studies,but also provide more pharmacodynamic biomarkers for disease prediction,diagnosis,and treatment.展开更多
AIM: To analyze proteomic and signal transduction alterations in irradiated melanoma cells. METHODS: We combined stable isotope labeling with amino acids in cell culture (SILAC) with highly sensitive shotgun tandem ma...AIM: To analyze proteomic and signal transduction alterations in irradiated melanoma cells. METHODS: We combined stable isotope labeling with amino acids in cell culture (SILAC) with highly sensitive shotgun tandem mass spectrometry (MS) to create an efficient approach for protein quantification. Protein protein interaction was used to analyze relationships among proteins. RESULTS: Energy metabolism protein levels were significantly different in glycolysis and not significantly different in oxidative phosphorylation after irradiation. Conversely, tumor suppressor proteins related to cell growth and development were downregulated, and those related to cell death and cell cycle were upregulated in irradiated cells. CONCLUSION: Our results indicate that irradiation induces differential expression of the 29 identified proteins closely related to cell survival, cell cycle arrest, and growth inhibition. The data may provide new insights into the pathogenesis of uveal melanoma and guide appropriate radiotherapy.展开更多
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 ...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展开更多
Dear Sir, I am Prof. Beuy Joob from Sanitation 1 Medical Academic Center, Bangkok, Thailand. I write to discuss the recent publication on proteomic analysis in diabetic retinopathy(DR).Liu et al [1] concluded that t...Dear Sir, I am Prof. Beuy Joob from Sanitation 1 Medical Academic Center, Bangkok, Thailand. I write to discuss the recent publication on proteomic analysis in diabetic retinopathy(DR).Liu et al [1] concluded that their approach by two dimensional fluorescence difference gel electrophoresis(2D-DIGE) combined with matrix-assisted laser展开更多
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...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展开更多
Hypoxic-ischemic encephalopathy,which predisposes to neonatal death and neurological sequelae,has a high morbidity,but there is still a lack of effective prevention and treatment in clinical practice.To better underst...Hypoxic-ischemic encephalopathy,which predisposes to neonatal death and neurological sequelae,has a high morbidity,but there is still a lack of effective prevention and treatment in clinical practice.To better understand the pathophysiological mechanism underlying hypoxic-ischemic encephalopathy,in this study we compared hypoxic-ischemic reperfusion brain injury and simple hypoxic-ischemic brain injury in neonatal rats.First,based on the conventional RiceVannucci model of hypoxic-ischemic encephalopathy,we established a rat model of hypoxic-ischemic reperfusion brain injury by creating a common carotid artery muscle bridge.Then we performed tandem mass tag-based proteomic analysis to identify differentially expressed proteins between the hypoxic-ischemic reperfusion brain injury model and the conventional Rice-Vannucci model and found that the majority were mitochondrial proteins.We also performed transmission electron microscopy and found typical characteristics of ferroptosis,including mitochondrial shrinkage,ruptured mitochondrial membranes,and reduced or absent mitochondrial cristae.Further,both rat models showed high levels of glial fibrillary acidic protein and low levels of myelin basic protein,which are biological indicators of hypoxic-ischemic brain injury and indicate similar degrees of damage.Finally,we found that ferroptosis-related Ferritin(Fth1)and glutathione peroxidase 4 were expressed at higher levels in the brain tissue of rats with hypoxic-ischemic reperfusion brain injury than in rats with simple hypoxic-ischemic brain injury.Based on these results,it appears that the rat model of hypoxic-ischemic reperfusion brain injury is more closely related to the pathophysiology of clinical reperfusion.Reperfusion not only aggravates hypoxic-ischemic brain injury but also activates the anti-ferroptosis system.展开更多
基金supported by the National Natural Science Foundation of China(31902298)the Shanxi Provincial Key Research and Development Program,China(2022ZDYF126)+2 种基金the Fund for Shanxi“1331 Project”,China(20211331-13)the Science and Technology Innovation Program of Shanxi Agricultural University,China(2017YJ10)the Special Research Fund of Shanxi Agricultural University for High-level Talents,China(2021XG001)。
文摘Evidence showed that N6-methyladenosine(m^(6)A)modification plays a pivotal role in influencing RNA fate and is strongly associated with cell growth and developmental processes in many species.However,no information regarding m^(6)A modification in Eimeria tenella is currently available.In the present study,we surveyed the transcriptome-wide prevalence of m^(6)A in sporulated oocysts and unsporulated oocysts of E.tenella.Methylated RNA immunoprecipitation sequencing(MeRIP-seq)analysis showed that m^(6)A modification was most abundant in the coding sequences,followed by stop codon.There were 3,903 hypermethylated and 3,178 hypomethylated mRNAs in sporulated oocysts compared with unsporulated oocysts.Further joint analysis suggested that m^(6)A modification of the majority of genes was positively correlated with mRNA expression.The mRNA relative expression and m^(6)A level of the selected genes were confirmed by quantitative reverse transcription PCR(RT-qPCR)and MeRIP-qPCR.GO and KEGG analysis indicated that differentially m^(6)A methylated genes(DMMGs)with significant differences in mRNA expression were closely related to processes such as regulation of gene expression,epigenetic,microtubule,autophagy-other and TOR signaling.Moreover,a total of 96 DMMGs without significant differences in mRNA expression showed significant differences at protein level.GO and pathway enrichment analysis of the 96 genes showed that RNA methylation may be involved in cell biosynthesis and metabolism of E.tenella.We firstly present a map of RNA m^(6)A modification in E.tenella,which provides significant insights into developmental biology of E.tenella.
基金Supported by the Natural Science Foundation of Shandong Province(No.ZR 2023 MD 059)the National Natural Science Foundation of China(No.41876135)。
文摘Previous studies have revealed that ammonia nitrogen has several adverse effects on clam Ruditapes philippinarum.However,knowledge is lacking regarding the related proteins involved in the toxicological responses,which is vital to elucidate the underlying mechanism of ammonia nitrogen.In this study,clams R.philippinarum were exposed to ammonia nitrogen for 21 d at two environmentally relevant concentrations.The tandem mass tags approach(TMT)was applied to assay the differentially expressed proteins(DEPs)in clam gill tissues on the 3 rd and 21 st day.Finally,a total of 7263 proteins were identified.Bioinformatics analyses revealed that clam protein profiles changed in dose-and time dependent manner after ammonia nitrogen exposure.We inferred that the clams may face heavy challenges after ammonia exposure,such as unbalanced gender ratio,lysosomal disease,energy lack,neurological disorders,altered glutamine metabolism,increased lipid synthesis,and impaired immunity.Variation profiles of enzyme activities of glutaminase and glutamine synthase provided direct evidence to verify the related inference from proteome data.Most of the inferred toxic effects merit further study.This study identified important proteins related to ammonia nitrogen toxicity in the clam and indicated the severe stress of marine ammonia pollution on the healthy development of mollusc aquaculture.
基金supported by grants from the National Science Foundation to J.H.(MCB 0618335MCB 1330441)and L.J.O.(MCB 0618279)
文摘Peroxisomes compartmentalize a dynamic suite of biochemical reactions and play a central role in plant metabolism, such as the degradation of hydrogen peroxide, metabolism of fatty acids, photorespiration, and the biosyn- thesis of plant hormones. Plant peroxisomes have been traditionally classified into three major subtypes, and in-depth mass spectrometry （MS）-based proteomics has been per- formed to explore the proteome of the two major subtypes present in green leaves and etiolated seedlings. Here, we carried out a comprehensive proteome analysis of perox- isomes from Arabidopsis leaves given a 48-h dark treatment. Our goal was to determine the proteome of the third major subtype of plant peroxisomes from senescent leaves, and further catalog the plant peroxisomal proteome. We identified a total of 111 peroxisomal proteins and verified the peroxisomal localization for six new proteins with potential roles in fatty acid metabolism and stress response by in vivo targeting analysis. Metabolic pathways compartmentalized in the three major subtypes of peroxisomes were also compared, which revealed a higher number of proteins involved in the detoxification of reactive oxygen species in peroxisomes from senescent leaves. Our study takes an important step towards mapping the full function of plant peroxisomes.
基金The study was funded by the financial support received from the Centre of Advanced Agricultural Science and Technology-National Agricultural Higher Education Project jointly funded by the World Bank and ICAR(Grant No.8776-IN-P151072).
文摘Phosphorus(P) deficiency limits the growth,development,and productivity of rice.To better understand the underlying mechanisms in P-deficiency tolerance and the role of Pup1 QTL in enhancing P use efficiency(PUE) for the development of P-efficient rice cultivars,a pair of contrasting rice genotypes(Pusa-44 and NIL-23) was applied to investigate the morpho-physio-biochemical and proteomic variation under P-starvation stress.The rice genotypes were grown hydroponically in a PusaRich medium with adequate P(16 mg/kg,+P) or without P(0 mg/kg,-P) for 30 d.P-starvation manifested a significant reductions in root and shoot biomass,shoot length,leaf area,total chlorophyll,and P,nitrogen and starch contents,as well as protein kinase activity.The stress increased root-to-shoot biomass ratio,root length,sucrose content,and acid phosphatase activity,particularly in the P-tolerant genotype(NIL-23).Comparative proteome analysis revealed several P metabolism-associated proteins(including OsCDPKs,OsMAPKs,OsCPKs,OsLecRK2,and OsSAPks) to be expressed in the shoot of NIL-23,indicating that multiple protein kinases were involved in P-starvation/deficiency tolerance.Moreover,the up-regulated expression of OsrbcL,OsABCG32,OsSUS5,OsPoll-like B,and ClpC2 proteins in the shoot,and OsACA9,OsACA8,OsSPS2F,OsPP2C15,and OsBiP3 in the root of NIL-23,indicated their role in P-starvation stress control through the Pup1 QTL. Thus,our findings indicated that-P stress-responsive proteins,in conjunction with morpho-physio-biochemical modulations,improved PUE and made NIL-23 a P-deficiency tolerant genotype due to the introgression of the Pup1 QTL in the Pusa-44 background.
基金supported by the National Natural Science Foundation of China(Nos.31471988 and 31200287)。
文摘The environmental characteristics of hypothermia and hypoxia exert great selective pressure on the energy metabolism of high-altitude animals,especially the ectotherms.Current research on energy-limited adaptation of high-altitude ectotherms has focused on energy expenditures.However,the mechanisms of increasing energy intake in high-altitude ectotherms have been studied rarely.In order to investigate the adaptation mechanism of the small intestine,the key part of energy acquisition for animals,to energy limitation at high altitude in ectotherms,the gut proteins of Phrynocephalus vlangalii from high-and low-altitude populations were compared using label free proteomics.GO enrichment and KEGG pathway analysis showed that proteins associated with energy intake,such as those involved in oxidation-reduction processes,glutathione metabolism,oxidoreductase activity,cofactor binding,catalytic activity and metabolic pathways,were significantly up-regulated in high-altitude populations;while proteins associated with energy expenditure,such as immune responses and processes,membrane attack complexes,natural killer pathway and other immune-related processes,were significantly down-regulated in expression.
文摘BACKGROUND The function of prohibitin 1(Phb1)during liver regeneration(LR)remains relatively unexplored.Our previous research identified downregulation of Phb1 in rat liver mitochondria 24 h after 70%partial hepatectomy(PHx),as determined by subcellular proteomic analysis.AIM To investigate the potential role of Phb1 during LR.METHODS We examined changes in Phb1 mRNA and protein levels,subcellular distribution,and abundance in rat liver during LR following 70%PHx.We also evaluated mitochondrial changes and apoptosis using electron microscopy and flow cytometry.RNA-interference-mediated knockdown of Phb1(PHBi)was performed in BRL-3A cells.RESULTS Compared with sham-operation control groups,Phb1 mRNA and protein levels in 70%PHx test groups were downregulated at 24 h,then upregulated at 72 and 168 h.Phb1 was mainly located in mitochondria,showed a reduced abundance at 24 h,significantly increased at 72 h,and almost recovered to normal at 168 h.Phb1 was also present in nuclei,with continuous increase in abundance observed 72 and 168 h after 70%PHx.The altered ultrastructure and reduced mass of mitochondria during LR had almost completely recovered to normal at 168 h.PHBi in BRL-3A cells resulted in increased S-phase entry,a higher number of apoptotic cells,and disruption of mitochondrial membrane potential.CONCLUSION Phb1 may contribute to maintaining mitochondrial stability and could play a role in regulating cell proliferation and apoptosis of rat liver cells during LR.
基金Supported by the Natural Science Foundation of China(No.20060109Z4016)the National Basic Research Development Program of China(No.2006CB101804)the Natural Science Foundation of Shandong Provincefor the excellent young researchers(No.2006BSA02004)
文摘Proteomics was used to reveal the differential protein expression profiles of acute responses to copper sulfate exposure in larvae of Artemia sinica.Fourteen differentially displayed protein spots were detected and seven of them were identified.Three spots were up-expressed and identified:actin, heat shock protein 70,and chaperone subunit 1;three down-regulated proteins were identified:arginine kinase,elongation factor-2,and glycine-rich protein;and a newly expressed protein was identified as peroxiredoxin.The study indicates the involvement of all the differentially expressed proteins in the early responses of protein expression,and in the survival of A.sinica in the presence of copper and other heavy metals;the findings improve understanding of the organism’s adaptive responses and resistance.
基金supported by grants from the National Natural Science Foundation of China(No.30471700)the "Tenth one five"Science and Technique Foundation of the PLA,China(No.06G027)
文摘BACKGROUND: Early diagnosis of liver metastasis of colorectal carcinoma is very important for the appropriate treatment of such patients. However, there has been no effective approach available for clinical application. The present study aimed to investigate the differential expression of proteins in patients with liver metastasis of colorectal carcinomas using proteomic analysis and evaluate its potentiality in clinical diagnosis. METHODS: Fluorescence two-dimensional differential in-gel electrophoresis (2-D DIGE) was used to analyze and compare the protein expression between normal mucosa, the primary focus, and liver metastases. Proteomic analysis was made to identify the differentially expressed proteins. Immunohistological staining was used to confirm the expression of differentially expressed proteins in colorectal carcinomas and areas of liver metastasis. RESULTS: A 1.5-fold difference was found with 46 differentially expressed proteins. In 20 differentially expressed proteins, 3 were down-regulated and 17 up-regulated in liver metastases. Proteomic analysis showed that the S-adenosylmethionine transgelin variant was down-regulated in liver metastasis tissues. Zinc finger protein 64 homolog (Zfp64), guanine nucleotide exchange factor 4 (GEF4), human arginase, glutathione S-transferases (GSTs) A3, and tumor necrosis factor a (TNF-alpha)-induced protein 9 were up-regulated in liver metastasis tissues. Immunohistochemical staining confirmed that human arginase expression was higher in liver metastases than in the primary focus. CONCLUSIONS: There was a significant difference in protein expression between the primary focus of colorectal carcinoma and liver metastases. The differentially regulated proteins were closely related to liver metastasis of colorectal carcinoma. Elevated human arginase may be an important molecular marker for liver metastasis from colorectal carcinoma. (Hepatobiliary Pancreat Dis Jut 2010; 9: 149-153)
基金Supported by the National Natural Science Foundation of China (30970089,20876181,20831006)the Natural Science Foundation of Guangdong Province (9351027501000003)
文摘Engineered Corynebacterium glutamicum was constructed for L-ornithine production by disrupting genes of argF and proB to prevent the flux away from L-ornithine.Effect of the inactivation of 2-oxoglutarate de-hydrogenase complex(ODHC) on L-ornithine production was also investigated.It was found that the inactivation of ODHC by knockout of the kgd gene enhanced L-ornithine production.The engineered C.glutamicum ATCC13032(ΔargFΔproBΔkgd) produced L-ornithine up to 4.78 g·L-1 from 0.24 g·L-1 of the wild-type strain.In order to understand the mechanism of L-ornithine production in C.glutamicum ATCC13032(ΔargFΔproBΔkgd) and find out new strategies for further enhancing L-ornithine production,the comparative proteome between the wild-type and the engineered strain was analyzed.L-Ornithine overproduction in the engineered strain was related to the up-regulation of the expression levels of enzymes involved in L-ornithine biosynthesis pathway and down-regulation of the expression levels of proteins involved in pentose phosphate pathway.The overexpression of genes in the upstream pathway of glutamate to increase the availability of endogenous glutamate may further in-crease ornithine production in the engineered C.glutamicum and the ornithine synthesis enzymes(ArgCJBD) may not be the limiting enzymes in the engineered C.glutamicum.
基金The Key Natural Science Foundation of Fujian under contract No. 2007J0004the National Natural Science Foundation of China under contract No. 40576076
文摘Viruses of thermophiles are of great interest due to their roles in gene transfer, global geochemical cycle and evolution of life on earth. However, the thermophilic bacteriophages have not been studied extensively. In this investigation, a typical bacteriophage BV1 was obtained from a thermophilic bacterium Geobacillus sp. 6k512, which was isolated from an inshore hot spring in Xiamen of China. The BV1 contained a double-stranded linear DNA of 35 055 bp, which encodes 54 open reading frames （ORFs）. Interestingly, eight of the 54 BV1 ORFs shared sequence similarities to genes from human disease-relevant bacteria. Seven proteins of the purified BV1 virions were identified by proteomic analysis. Determination of BV1 functional genomics would facilitate the better understanding of the mechanism for virus-thermophile interaction.
基金supported by the Natural Science Foundation of Fujian Province,China,No.2015J05153Research Talents Training Project of Fujian Provincial Health Department,China,No.2018-ZQN-29Joint Funds for the Innovation of Science and Technology of Fujian Province,China,No.2018Y9002(all to WHC).
文摘Our previous study has confirmed that astrocytes overexpressing neurogenic differentiation factor 1(NEUROD1)in the spinal cord can be reprogrammed into neurons under in vivo conditions.However,whether they can also be reprogrammed into neurons under in vitro conditions remains unclear,and the mechanisms of programmed conversion from astrocytes to neurons have not yet been clarified.In the present study,we prepared reactive astrocytes from newborn rat spinal cord astrocytes using the scratch method and infected them with lentivirus carrying NEUROD1.The results showed that NEUROD1 overexpression reprogrammed the cultured reactive astrocytes into neurons in vitro with an efficiency of 13.4%.Using proteomic and bioinformatic analyses,1952 proteins were identified,of which 92 were differentially expressed.Among these proteins,11 were identified as candidate proteins in the process of reprogramming based on their biological functions and fold-changes in the bioinformatic analysis.Furthermore,western blot assay revealed that casein kinase II subunit alpha(CSNK2A2)and pinin(PNN)expression in NEUROD1-overexpressing reactive astrocytes was significantly increased,suggesting that NEUROD1 can directly reprogram spinal cord-derived reactive astrocytes into neurons in vitro,and that the NEUROD1-CSNK2A2-PNN pathway is involved in this process.This study was approved by the Animal Ethics Committee of Fujian Medical University,China(approval No.2016-05)on April 18,2016.
基金Supported by the National Natural Science Foundation of China(No.81671641)Suzhou Science and Technology Fund of China(No.SYS2020137)。
文摘AIM:To analyze the retinal proteomes with and without conbercept treatments in mice with oxygen-induced retinopathy(OIR)and identify proteins involved in the molecular mechanisms mediated by conbercept.METHODS:OIR was induced in fifty-six C57 BL/6 J mouse pups and randomly divided into four groups.Group 1:Normal17(n=7),mice without OIR and treated with normal air.Group 2:OIR12/EXP1(n=14),mice received 75%oxygen from postnatal day(P)7 to 12.Group 3:OIR17/Control(n=14),mice received 75%oxygen from P7 to P12 and then normal air to P17.Group 4:Lang17/EXP2(n=21),mice received 75%oxygen from P7 to P12 with intravitreal injection of 1μL conbercept at the concentration of 10 mg/m L at P12,and then normal air from P12 to P17.Liquid ChromatographyMass Spectrometry(LC-MS)/MS data were reviewed to find proteins that were up-regulated after the conbercept treatment.Gene ontology(GO)analysis was performed of conbercept-mediated changes in proteins involved in single-organism processes,biological regulation,cellular processes,immune responses,metabolic processes,locomotion and multiple-organism processes.RESULTS:Conbercept induced a reversal of hypoxiainducible factor 1 signaling pathway as revealed by the Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis and also induced down-regulation of proteins involved in blood coagulation and fibrin clot formation as demonstrated by the Database for Annotation,Visualization and Integrated Discovery(DAVID)and the stimulation of interferon genes studies.These appear to be risk factors of retinal fibrosis.Additional conbercept-specific fibrosis risk factors were also identified and may serve as therapeutic targets for fibrosis.CONCLUSION:Our studies reveal that many novel proteins are differentially regulated by conbercept.The new insights may warrant a valuable resource for conbercept treatment.
基金This study was supported by the National Natural Science Foundation of China(82074367).
文摘Background:Guben Zhike decoction(GBZKD)is derived from the experience of Professor Enxiang Chao,an esteemed master of Chinese medicine,while treating chronic obstructive pulmonary disease(COPD).GBZKD reinforces the healthy qi and consolidates defensive qi.This study explored the efficacy and potential mechanism of action of GBZKD in a COPD mouse model using proteomics.Methods:A COPD mouse model was established through cigarette smoke exposure and intranasal lipopolysaccharide administration.The model was verified through lung function test and lung histopathological observation.Label-free quantitative proteomics was used to detect the lung tissue proteins of mice from the GBZKD,COPD,and control groups.Results:GBZKD markedly improved the lung function and associated pathological conditions in the COPD mouse model.Proteomic analysis identified 4316 proteins,of which 3696 were quantitative proteins.We highlighted 287 and 184 proteins with significant regulatory roles in the lung tissues of COPD mice and GBZKD-treated mice,respectively.These proteins participated in multiple functions,including complement/coagulation cascade,immune response,and metabolic pathways.Conclusion:GBZKD exhibits multitarget and multipathway therapeutic effects in a COPD mouse model.
文摘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
基金support from the National Key Research and Development Program of China(Grant Nos.:2020YFA0908000 and 2020YFE0205100)the Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine(Grant No.:ZYYCXTD-C-202002)+3 种基金the National Natural Science Foundation of China(Grant Nos.:82074098,82173914,and 82141001)the CACMS Innovation Fund(Grant Nos.:CI2021A05101 and CI2021A05104)the Fundamental Research Funds for the Central Public Welfare Research Institutes(Grant Nos.:ZZ15-YQ-065,ZZ14-YQ-058,ZZ14-YQ-050,ZZ14-YQ-051,ZZ14-YQ-052,ZZ14-ND-010,ZZ15-ND-10,and ZZ14-FL-002)the Chinese Academy of Sciences(Grant No.:YJKYYQ20210025).
文摘The composition of serum is extremely complex,which complicates the discovery of new pharmacodynamic biomarkers via serum proteome for disease prediction and diagnosis.Recently,nanoparticles have been reported to efficiently reduce the proportion of high-abundance proteins and enrich lowabundance proteins in serum.Here,we synthesized a silica-coated iron oxide nanoparticle and developed a highly efficient and reproducible protein corona(PC)-based proteomic analysis strategy to improve the range of serum proteomic analysis.We identified 1,070 proteins with a median coefficient of variation of 12.56%using PC-based proteomic analysis,which was twice the number of proteins identified by direct digestion.There were also more biological processes enriched with these proteins.We applied this strategy to identify more pharmacodynamic biomarkers on collagen-induced arthritis(CIA)rat model treated with methotrexate(MTX).The bioinformatic results indicated that 485 differentially expressed proteins(DEPs)were found in CIA rats,of which 323 DEPs recovered to near normal levels after treatment with MTX.This strategy can not only help enhance our understanding of the mechanisms of disease and drug action through serum proteomics studies,but also provide more pharmacodynamic biomarkers for disease prediction,diagnosis,and treatment.
基金The Foundation for Young Talents of Gansu Province, China (No. 1208RJYA013)
文摘AIM: To analyze proteomic and signal transduction alterations in irradiated melanoma cells. METHODS: We combined stable isotope labeling with amino acids in cell culture (SILAC) with highly sensitive shotgun tandem mass spectrometry (MS) to create an efficient approach for protein quantification. Protein protein interaction was used to analyze relationships among proteins. RESULTS: Energy metabolism protein levels were significantly different in glycolysis and not significantly different in oxidative phosphorylation after irradiation. Conversely, tumor suppressor proteins related to cell growth and development were downregulated, and those related to cell death and cell cycle were upregulated in irradiated cells. CONCLUSION: Our results indicate that irradiation induces differential expression of the 29 identified proteins closely related to cell survival, cell cycle arrest, and growth inhibition. The data may provide new insights into the pathogenesis of uveal melanoma and guide appropriate radiotherapy.
文摘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
文摘Dear Sir, I am Prof. Beuy Joob from Sanitation 1 Medical Academic Center, Bangkok, Thailand. I write to discuss the recent publication on proteomic analysis in diabetic retinopathy(DR).Liu et al [1] concluded that their approach by two dimensional fluorescence difference gel electrophoresis(2D-DIGE) combined with matrix-assisted laser
文摘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
基金supported by the National Natural Science Foundation of China,No.82271747(to ZLL)Medical and Health Science and Technology Program of Zhejiang Province of China,No.2023RC048(to WL)。
文摘Hypoxic-ischemic encephalopathy,which predisposes to neonatal death and neurological sequelae,has a high morbidity,but there is still a lack of effective prevention and treatment in clinical practice.To better understand the pathophysiological mechanism underlying hypoxic-ischemic encephalopathy,in this study we compared hypoxic-ischemic reperfusion brain injury and simple hypoxic-ischemic brain injury in neonatal rats.First,based on the conventional RiceVannucci model of hypoxic-ischemic encephalopathy,we established a rat model of hypoxic-ischemic reperfusion brain injury by creating a common carotid artery muscle bridge.Then we performed tandem mass tag-based proteomic analysis to identify differentially expressed proteins between the hypoxic-ischemic reperfusion brain injury model and the conventional Rice-Vannucci model and found that the majority were mitochondrial proteins.We also performed transmission electron microscopy and found typical characteristics of ferroptosis,including mitochondrial shrinkage,ruptured mitochondrial membranes,and reduced or absent mitochondrial cristae.Further,both rat models showed high levels of glial fibrillary acidic protein and low levels of myelin basic protein,which are biological indicators of hypoxic-ischemic brain injury and indicate similar degrees of damage.Finally,we found that ferroptosis-related Ferritin(Fth1)and glutathione peroxidase 4 were expressed at higher levels in the brain tissue of rats with hypoxic-ischemic reperfusion brain injury than in rats with simple hypoxic-ischemic brain injury.Based on these results,it appears that the rat model of hypoxic-ischemic reperfusion brain injury is more closely related to the pathophysiology of clinical reperfusion.Reperfusion not only aggravates hypoxic-ischemic brain injury but also activates the anti-ferroptosis system.
