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 ...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.展开更多
The cumulative damage caused by repetitive mild traumatic brain injury can cause long-term neurodegeneration leading to cognitive impairment.This cognitive impairment is thought to result specifically from damage to t...The cumulative damage caused by repetitive mild traumatic brain injury can cause long-term neurodegeneration leading to cognitive impairment.This cognitive impairment is thought to result specifically from damage to the hippocampus.In this study,we detected cognitive impairment in mice 6 weeks after repetitive mild traumatic brain injury using the novel object recognition test and the Morris water maze test.Immunofluorescence staining showed that p-tau expression was increased in the hippocampus after repetitive mild traumatic brain injury.Golgi staining showed a significant decrease in the total density of neuronal dendritic spines in the hippocampus,as well as in the density of mature dendritic spines.To investigate the specific molecular mechanisms underlying cognitive impairment due to hippocampal damage,we performed proteomic and phosphoproteomic analyses of the hippocampus with and without repetitive mild traumatic brain injury.The differentially expressed proteins were mainly enriched in inflammation,immunity,and coagulation,suggesting that non-neuronal cells are involved in the pathological changes that occur in the hippocampus in the chronic stage after repetitive mild traumatic brain injury.In contrast,differentially expressed phosphorylated proteins were mainly enriched in pathways related to neuronal function and structure,which is more consistent with neurodegeneration.We identified N-methyl-D-aspartate receptor 1 as a hub molecule involved in the response to repetitive mild traumatic brain injury,and western blotting showed that,while N-methyl-D-aspartate receptor 1 expression was not altered in the hippocampus after repetitive mild traumatic brain injury,its phosphorylation level was significantly increased,which is consistent with the omics results.Administration of GRP78608,an N-methyl-D-aspartate receptor 1 antagonist,to the hippocampus markedly improved repetitive mild traumatic brain injury-induced cognitive impairment.In conclusion,our findings suggest that N-methyl-D-aspartate receptor 1 sig展开更多
Sweet and umami tastes are elicited by sweet and umami receptors on the tongue and palate epithelium,respectively.However,the molecular machinery allowing the taste reaction remains incompletely understood.Through a p...Sweet and umami tastes are elicited by sweet and umami receptors on the tongue and palate epithelium,respectively.However,the molecular machinery allowing the taste reaction remains incompletely understood.Through a phosphoproteomic approach,we identified the key proteins that trigger taste mechanisms based on phosphorylation cascades.Ryanodine receptor isoform 1(RYR1)was further verified by sensory and behavioral assays.We propose a model of RYR1-mediated sweet/umami signaling in which the RYR1 channel,which mediates Ca^(2+)release from the endoplasmic reticulum,is closed by dephosphorylation in bud tissue after sweet/umami treatment.The alteration in Ca^(2+)content in the cytosol induces transient membrane depolarization and generates a cell current for taste signal transduction.We demonstrate that RYR1 is a new channel involved in the regulation of sweet/umami signal transduction and propose a“metabolic clock”notion based on sweet/umami sensing.Our study provides a valuable foundation for a system-level understanding of the taste perception mechanism.展开更多
Salinity severely affects plant growth and development.Thus,it is crucial to identify the genes functioning in salt stress response and unravel the mechanism by which plants against salt stress.This study used the pho...Salinity severely affects plant growth and development.Thus,it is crucial to identify the genes functioning in salt stress response and unravel the mechanism by which plants against salt stress.This study used the phosphoproteomic assay and found that 123 of the 4000 quantitative analyzed phosphopeptides were induced by salt stress.The functional annotation of the non-redundant protein database(NR)showed 23 differentially expressed transcription factors,including a phosphopeptide covering the Serine 31 in the RAV(related to ABI3/VP1)transcription factor(named SiRAV1).SiRAV1 was located in the nucleus.Phenotypic and physiological analysis showed that overexpressing SiRAV1 in foxtail millet enhanced salt tolerance and alleviated the salt-induced increases of H_(2)O_(2) accumulation,malondialdehyde(MDA)content,and percent of electrolyte leakage.Further analysis showed that SiRAV1 positively regulated SiCAT expression to modulate the catalase(CAT)activity by directly binding to the SiCAT promoter in vivo and in vitro.Moreover,we found that phosphorylation of SiRAV1 at the Ser31 site positively regulated salt tolerance in foxtail millet via enhancing its binding ability to SiCAT promoter but did not affect its subcellular localization.Overall,our results define a mechanism for SiRAV1 function in salt response where salt-triggered phosphorylation of SiRAV1 at Ser31 enhances its binding ability to SiCAT promoter,and the increased SiCAT expression contributes to salt tolerance in foxtail millet.展开更多
Dietary threonine(Thr)deficiency enhances triglyceride(TG)deposition in the liver of Pekin ducks,which injures hepatic function and impairs growth performance.However,the underlying molecular mechanisms remain unclear...Dietary threonine(Thr)deficiency enhances triglyceride(TG)deposition in the liver of Pekin ducks,which injures hepatic function and impairs growth performance.However,the underlying molecular mechanisms remain unclear.In the present study,we investigated the effects of dietary Thr deficiency on the expressions of proteins and phosphoproteins in liver of Pekin ducks,to identify the underlying molecular changes.A total of 300 one-day-old ducklings were divided into 3 groups with 10 replicates of 10 birds.All ducks were fed corn-wheat-peanut meal diets containing 0.46%,0.71%,and 0.96%Thr,respectively,from 1 to 21 days of age.Growth performance,serum parameters,hepatic TG content,and expression of genes involved in lipid metabolism of Pekin ducks were determined.A Thr deficiency group(Thr-D,0.46%Thr)and a Thr sufficiency group(Thr-S,0.71%Thr)were selected for subsequent proteomic and phosphoproteomic analysis.The results showed that Thr-D reduced the growth performance(P<0.001),and increased the plasma concentrations of cholesterol,high-density lipoprotein cholesterol,low-density lipoprotein cholesterol,and hepatic TG(P<0.05).Thr-D increased gene expression related to fatty acid and TG synthesis(P<0.05).A total of 176 proteins and 259 phosphosites(containing 198 phosphoproteins)were observed to be differentially expressed as a result of Thr-D.The upregulated proteins were enriched in the pathway related to amino acid metabolism,peroxisome.The down-regulated proteins were enriched in linolenic and arachidonic acid metabolism,and the Janus kinase-signal transducer and activator of transcription(JAK-STAT)signaling pathway.The upregulated phos-phoproteins were enriched in the pathways related to fatty acid biosynthesis,fructose and mannose metabolism,and glycolysis/gluconeogenesis.Thr-D reduced the phosphorylation of STAT1 at S729 and STAT3 at S728,and expression of STAT5B.In contrast,Thr-D increased non-receptor tyrosine-protein kinase(TYK2)expression and STAT1 phosphorylation at S649.Taken together,dietary Thr-D increa展开更多
Over the past decade,systems biology and plant-omics have increasingly become the main stream in plant biology research.New developments in mass spectrometry and bioinformatics tools,and methodological schema to inte-...Over the past decade,systems biology and plant-omics have increasingly become the main stream in plant biology research.New developments in mass spectrometry and bioinformatics tools,and methodological schema to inte-grate multi-omics data have leveraged recent advances in proteomics and metabolomics.These progresses are driv-ing a rapid evolution in the field of plant research,greatly facilitating our understanding of the mechanistic aspects of plant metabolisms and the interactions of plants with their external environment.Here,we review the recent progresses in MS-based proteomics and metabolomics tools and workflows with a special focus on their applications to plant biology research using several case studies related to mechanistic understanding of stress response,gene/protein function characterization,metabolic and signaling pathways exploration,and natural product discovery.We also present a projection concerning future perspectives in MS-based proteomics and metabolomics development including their applications to and challenges for system biology.This review is intended to provide readers with an overview of how advanced MS technology,and integrated application of proteomics and metabolomics can be used to advance plant system biology research.展开更多
Protein phosphorylation,one of the major post-translational modifications,plays a crucial role in cell signaling,DNA replication,gene expression and differentiation;and alters enzyme activity and other biological acti...Protein phosphorylation,one of the major post-translational modifications,plays a crucial role in cell signaling,DNA replication,gene expression and differentiation;and alters enzyme activity and other biological activities;and regulates cell proliferation and enlargement,phytohormone biosynthesis and signaling,plant disease resistance,and grain filling and quality during rice seed development.Research work on protein phosphorylation started in the 1950 s with the discovery of phosphorylase a and phosphorylase b which are phospho and dephospho forms of the same enzyme.Over the last decade,rice proteomics has accomplished tremendous progress in setting up techniques to proteome nearly all tissues,organs and organelles.The progress made in this field is evident in number of research works.However,research on rice protein phosphorylation is still at its infancy and there are still many unanswered questions.In this review,the general description of protein phosphorylation,including history,structure,frequency of occurrence and function,are discussed.This work also elucidates the different methods for identification,qualification and finally,the progress in rice phosphoproteome research and perspectives.展开更多
文摘目的:探究小鼠颞叶癫痫慢性发作期蛋白质功能和信号通路的改变。方法:(1)制备小鼠卡英酸颞叶癫痫模型,行为学达到Racine分级4分判定为造模成功。28 d后,取对照组和实验组小鼠海马组织进行磷酸化蛋白组学实验;(2)选取检出密度大于106的数据进行统计分析;(3)利用GO(Gene Ontology)数据库、KEGG(Kyoto Encyclopedia of Genes and Genomes)数据库和STRING数据库对磷酸化蛋白组学数据进行统计分析;(4)结合文献对组学结果进行分析。结果:(1)质谱共检测出12 697个蛋白质磷酸化位点,其中159个位点变化差异具有统计学意义(P<0.05);(2)在蛋白质功能层面,磷酸化水平显著性变化的蛋白质的分子功能主要是结合(39.5%)和催化活性(35.7%),这些蛋白质参与细胞交流(20.8%)、初级代谢和含磷酸盐化合物代谢等生化过程;(3)在信号通路层面,这些蛋白质参与10条信号转导通路,包括谷氨酸能突触信号通路、Ras信号通路、长时程增强信号通路等;(4)在蛋白质相互作用层面,这些蛋白质形成以Grin1和Dlg3为核心,以Arhgef 2、Arhgap33和Tiam1为核心与以Spnb1/3/4、Add3和Ank2为核心的蛋白质相互作用网;(5)磷酸化蛋白组学数据显示,Grin1、Arhgef2、Arhgap33、Tiam1、Sptbn1/2/4和Ank2等磷酸化水平在癫痫慢性发作期显著升高。结论:磷酸化蛋白组学的结果从蛋白质功能、信号通路和蛋白质相互作用3个层面阐明了小鼠颞叶癫痫慢性发作期海马体蛋白质的变化,验证了磷酸化蛋白组学研究的可靠性,并提示多巴胺功能和Kir3.1钾通道功能可能与癫痫发生相关。
基金supported by the National Natural Science Foundation of China(32001110)Training Program for Cultivating Highlevel Talents by the China Scholarship Council(2021lxjjw01)Open Project of State Key Laboratory of Plateau Ecology and Agriculture,Qinghai University(2021-KF-004)。
文摘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.
基金funded by the National Natural Science Foundation of China,Nos.82171363(to PL),82171321(to XL),82171458(to XJ)the Youth Nova Program of Shaanxi,No.2021KJXX-19(to PL)。
文摘The cumulative damage caused by repetitive mild traumatic brain injury can cause long-term neurodegeneration leading to cognitive impairment.This cognitive impairment is thought to result specifically from damage to the hippocampus.In this study,we detected cognitive impairment in mice 6 weeks after repetitive mild traumatic brain injury using the novel object recognition test and the Morris water maze test.Immunofluorescence staining showed that p-tau expression was increased in the hippocampus after repetitive mild traumatic brain injury.Golgi staining showed a significant decrease in the total density of neuronal dendritic spines in the hippocampus,as well as in the density of mature dendritic spines.To investigate the specific molecular mechanisms underlying cognitive impairment due to hippocampal damage,we performed proteomic and phosphoproteomic analyses of the hippocampus with and without repetitive mild traumatic brain injury.The differentially expressed proteins were mainly enriched in inflammation,immunity,and coagulation,suggesting that non-neuronal cells are involved in the pathological changes that occur in the hippocampus in the chronic stage after repetitive mild traumatic brain injury.In contrast,differentially expressed phosphorylated proteins were mainly enriched in pathways related to neuronal function and structure,which is more consistent with neurodegeneration.We identified N-methyl-D-aspartate receptor 1 as a hub molecule involved in the response to repetitive mild traumatic brain injury,and western blotting showed that,while N-methyl-D-aspartate receptor 1 expression was not altered in the hippocampus after repetitive mild traumatic brain injury,its phosphorylation level was significantly increased,which is consistent with the omics results.Administration of GRP78608,an N-methyl-D-aspartate receptor 1 antagonist,to the hippocampus markedly improved repetitive mild traumatic brain injury-induced cognitive impairment.In conclusion,our findings suggest that N-methyl-D-aspartate receptor 1 sig
基金supported by the National Natural Science Foundation of China(31972198,31622042,31901813,31671857,31901782).
文摘Sweet and umami tastes are elicited by sweet and umami receptors on the tongue and palate epithelium,respectively.However,the molecular machinery allowing the taste reaction remains incompletely understood.Through a phosphoproteomic approach,we identified the key proteins that trigger taste mechanisms based on phosphorylation cascades.Ryanodine receptor isoform 1(RYR1)was further verified by sensory and behavioral assays.We propose a model of RYR1-mediated sweet/umami signaling in which the RYR1 channel,which mediates Ca^(2+)release from the endoplasmic reticulum,is closed by dephosphorylation in bud tissue after sweet/umami treatment.The alteration in Ca^(2+)content in the cytosol induces transient membrane depolarization and generates a cell current for taste signal transduction.We demonstrate that RYR1 is a new channel involved in the regulation of sweet/umami signal transduction and propose a“metabolic clock”notion based on sweet/umami sensing.Our study provides a valuable foundation for a system-level understanding of the taste perception mechanism.
基金This work was funded by the National Natural Science Foundation of China(31902062)the South China Botanical Garden,Chinese Academy of Sciences(QNXM-02).
文摘Salinity severely affects plant growth and development.Thus,it is crucial to identify the genes functioning in salt stress response and unravel the mechanism by which plants against salt stress.This study used the phosphoproteomic assay and found that 123 of the 4000 quantitative analyzed phosphopeptides were induced by salt stress.The functional annotation of the non-redundant protein database(NR)showed 23 differentially expressed transcription factors,including a phosphopeptide covering the Serine 31 in the RAV(related to ABI3/VP1)transcription factor(named SiRAV1).SiRAV1 was located in the nucleus.Phenotypic and physiological analysis showed that overexpressing SiRAV1 in foxtail millet enhanced salt tolerance and alleviated the salt-induced increases of H_(2)O_(2) accumulation,malondialdehyde(MDA)content,and percent of electrolyte leakage.Further analysis showed that SiRAV1 positively regulated SiCAT expression to modulate the catalase(CAT)activity by directly binding to the SiCAT promoter in vivo and in vitro.Moreover,we found that phosphorylation of SiRAV1 at the Ser31 site positively regulated salt tolerance in foxtail millet via enhancing its binding ability to SiCAT promoter but did not affect its subcellular localization.Overall,our results define a mechanism for SiRAV1 function in salt response where salt-triggered phosphorylation of SiRAV1 at Ser31 enhances its binding ability to SiCAT promoter,and the increased SiCAT expression contributes to salt tolerance in foxtail millet.
基金supported by National Natural Science Foundation of China(31902174)Natural Science Foundation of Jiangsu Province(BK20190902)Tackled key technologies in agriculture and rural areas of Jiangsu Science and Technology Plan(BE2022310).
文摘Dietary threonine(Thr)deficiency enhances triglyceride(TG)deposition in the liver of Pekin ducks,which injures hepatic function and impairs growth performance.However,the underlying molecular mechanisms remain unclear.In the present study,we investigated the effects of dietary Thr deficiency on the expressions of proteins and phosphoproteins in liver of Pekin ducks,to identify the underlying molecular changes.A total of 300 one-day-old ducklings were divided into 3 groups with 10 replicates of 10 birds.All ducks were fed corn-wheat-peanut meal diets containing 0.46%,0.71%,and 0.96%Thr,respectively,from 1 to 21 days of age.Growth performance,serum parameters,hepatic TG content,and expression of genes involved in lipid metabolism of Pekin ducks were determined.A Thr deficiency group(Thr-D,0.46%Thr)and a Thr sufficiency group(Thr-S,0.71%Thr)were selected for subsequent proteomic and phosphoproteomic analysis.The results showed that Thr-D reduced the growth performance(P<0.001),and increased the plasma concentrations of cholesterol,high-density lipoprotein cholesterol,low-density lipoprotein cholesterol,and hepatic TG(P<0.05).Thr-D increased gene expression related to fatty acid and TG synthesis(P<0.05).A total of 176 proteins and 259 phosphosites(containing 198 phosphoproteins)were observed to be differentially expressed as a result of Thr-D.The upregulated proteins were enriched in the pathway related to amino acid metabolism,peroxisome.The down-regulated proteins were enriched in linolenic and arachidonic acid metabolism,and the Janus kinase-signal transducer and activator of transcription(JAK-STAT)signaling pathway.The upregulated phos-phoproteins were enriched in the pathways related to fatty acid biosynthesis,fructose and mannose metabolism,and glycolysis/gluconeogenesis.Thr-D reduced the phosphorylation of STAT1 at S729 and STAT3 at S728,and expression of STAT5B.In contrast,Thr-D increased non-receptor tyrosine-protein kinase(TYK2)expression and STAT1 phosphorylation at S649.Taken together,dietary Thr-D increa
基金This research was supported by the Key Realm R&D Program of Guangdong Province(No.2020B0202090005)the Science and Technology Program of Guangdong Province(2021A0505030050)+2 种基金the Project of Collaborative Innovation Center of Guangdong Academy of Agricultural Sciences(XTXM202203)the Special Fund for Scientific Innovation Strategy-construction of High-Level Academy of Agriculture Science(No.R2020PY-JX019,R2021YJ-QG004)two USDA grants(No.8062-21000-046-00D and No.8062-21000-047-00D)。
文摘Over the past decade,systems biology and plant-omics have increasingly become the main stream in plant biology research.New developments in mass spectrometry and bioinformatics tools,and methodological schema to inte-grate multi-omics data have leveraged recent advances in proteomics and metabolomics.These progresses are driv-ing a rapid evolution in the field of plant research,greatly facilitating our understanding of the mechanistic aspects of plant metabolisms and the interactions of plants with their external environment.Here,we review the recent progresses in MS-based proteomics and metabolomics tools and workflows with a special focus on their applications to plant biology research using several case studies related to mechanistic understanding of stress response,gene/protein function characterization,metabolic and signaling pathways exploration,and natural product discovery.We also present a projection concerning future perspectives in MS-based proteomics and metabolomics development including their applications to and challenges for system biology.This review is intended to provide readers with an overview of how advanced MS technology,and integrated application of proteomics and metabolomics can be used to advance plant system biology research.
文摘Protein phosphorylation,one of the major post-translational modifications,plays a crucial role in cell signaling,DNA replication,gene expression and differentiation;and alters enzyme activity and other biological activities;and regulates cell proliferation and enlargement,phytohormone biosynthesis and signaling,plant disease resistance,and grain filling and quality during rice seed development.Research work on protein phosphorylation started in the 1950 s with the discovery of phosphorylase a and phosphorylase b which are phospho and dephospho forms of the same enzyme.Over the last decade,rice proteomics has accomplished tremendous progress in setting up techniques to proteome nearly all tissues,organs and organelles.The progress made in this field is evident in number of research works.However,research on rice protein phosphorylation is still at its infancy and there are still many unanswered questions.In this review,the general description of protein phosphorylation,including history,structure,frequency of occurrence and function,are discussed.This work also elucidates the different methods for identification,qualification and finally,the progress in rice phosphoproteome research and perspectives.
