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
Background：The molecular mechanisms underlying the endometriosis are still not completely understood.In order to test the hypothesis that the approaches in phosphoproteomics might contribute to the identification of ...Background：The molecular mechanisms underlying the endometriosis are still not completely understood.In order to test the hypothesis that the approaches in phosphoproteomics might contribute to the identification of key biomarkers to assess disease pathogenesis and drug targets,we carried out a phosphoproteomics analysis of human endometrium.Methods：A large-scale differential phosphoproteome analysis,using peptide enrichment of titanium dioxide purify and sequential elution from immobilized metal affinity chromatography with linear trap quadrupole-tandem mass spectrometry,was performed in endometrium tissues from 8 women with or without endometriosis.Results：The phosphorylation profiling of endometrium from endometriosis patients had been obtained,and found that identified 516 proteins were modified at phosphorylation level during endometriosis.Gene ontology annotation analysis showed that these proteins were enriched in cellular processes of binding and catalytic activity.Further pathway analysis showed that ribosome pathway and focal adhesion pathway were the top two pathways,which might be deregulated during the development of endometriosis.Conclusions：That large-scale phosphoproteome quantification has been successfully identified in endometrium tissues of women with or without endometriosis will provide new insights to understand the molecular mechanisms of the development of endometriosis.展开更多
De-etiolation consists of a series of developmental and physiological changes that a plant undergoes in response to light.During this process light,an important environmental signal,triggers the inhibition of mesocoty...De-etiolation consists of a series of developmental and physiological changes that a plant undergoes in response to light.During this process light,an important environmental signal,triggers the inhibition of mesocotyl elongation and the production of photosynthetically active chloroplasts,and etiolated leaves transition from the"sink"stage to the"source"stage.De-etiolation has been extensively studied in maize(Zea mays L.).However,little is known about how this transition is regulated.In this study,we described a quantitative proteomic and phosphoproteomic atlas of the de-etiolation process in maize.We identified 16,420 proteins in proteome,among which 14,168 proteins were quantified.In addition,8746 phosphorylation sites within 3110 proteins were identified.From the combined proteomic and phosphoproteomic data,we identified a total of 17,436 proteins.Only 7.0%(998/14,168)of proteins significantly changed in abundance during de-etiolation.In contrast,26.6%of phosphorylated proteins exhibited significant changes in phosphorylation level;these included proteins involved in gene expression and homeostatic pathways and rate-limiting enzymes involved in photosynthetic light and carbon reactions.Based on phosphoproteomic analysis,34.0%(1057/3110)of phosphorylated proteins identified in this study contained more than 2 phosphorylation sites,and 37 proteins contained more than 16 phosphorylation sites,indicating that multi-phosphorylation is ubiquitous during the de-etiolation process.Our results suggest that plants might preferentially regulate the level of posttranslational modifications(PTMs)rather than protein abundance for adapting to changing environments.The study of PTMs could thus better reveal the regulation of de-etiolation.展开更多
We now know that 11 different families of cyclic nucleotide phosphodiesterases(PDEs) are expressed in mammalian species. Most of these families contain multiple gene products and most of the genes utilize alternative ...We now know that 11 different families of cyclic nucleotide phosphodiesterases(PDEs) are expressed in mammalian species. Most of these families contain multiple gene products and most of the genes utilize alternative splicing or alternative start sites to encode more than one RNA/protein.However,specific functions for these different PDEs have not yet been identified in most cell types despite the fact that selective inhibitors to most of the PDE families are available. Conventional approaches to study PDE function typically rely on measurements of global cAMP,or general increases in cAMP-dependent protein kinase A(PKA),or exchange protein activated by cAMP(EPAC) activity.Although newer approaches utilizing subcellularly-targeted FRET reporter sensors have helped to define more compartmentalized regulation of cAMP,PKA,and EPAC,they have limited ability to link this regulation to downstream effector molecules and biological functions. To address this problem,we have begun to use an unbiased,mass spectrometry-based approach coupled with treatment using PDE isozyme-selective inhibitors to characterize the phosphoproteomes of the ″ functional pools″ of cAMP that are regulated by specific cAMP-PDEs(the PDE-regulated phosphoproteomes). In MA-10 Leydig cells we find that in order to detect appreciable increased in either phosphorylation or steroid production,one needs to inhibit both PDE 4 and PDE 8 activity.Using this combination of inhibitors,we find large PDE inhibitor-induced changes in many different proteins that modulate steroid trafficking and biosynthesis. The data are consistent with the idea that cAMP serves to coordinate hormone stimulation of steroid production by altering the phosphorylation of many different proteins at multiple points in the overall pathway rather than just controlling a single rate limiting step. It seems quite likely that many of the proteins phosphorylated in this cell type in response to PDE inhibition,will also be regulated by cAMP in many other cell types.Similarly,in Jurkat ce展开更多
Brassinosteroid(BR), a steroid phytohormone, whose signaling transduction pathways include a series of phosphorylation and dephosphorylation events, and GSK3 s are the main negative regulator kinases. BRs have been sh...Brassinosteroid(BR), a steroid phytohormone, whose signaling transduction pathways include a series of phosphorylation and dephosphorylation events, and GSK3 s are the main negative regulator kinases. BRs have been shown to play vital roles in cotton fiber elongation. However, the underlying mechanism is still elusive. In this study, fibers of a BR-defective mutant Pagoda 1(pag1), and its corresponding wild-type(ZM24) were selected for a comparative global phosphoproteome analysis at critical developmental time points: fast-growing stage(10 days after pollination(DPA)) and secondary cell wall synthesis stage(20DPA). Based on the substrate characteristics of GSK3, 900 potential substrates were identified. Their GO and KEGG annotation results suggest that BR functions in fiber development by regulating GhSKs(GSK3s of Gossypium hirsutum L.) involved microtubule cytoskeleton organization, and pathways of glucose, sucrose and lipid metabolism. Further experimental results revealed that among the GhSK members identified, GhSK13 not only plays a role in BR signaling pathway, but also functions in developing fiber by respectively interacting with an AP2-like ethylene-responsive factor GhAP2L, a nuclear transcription factor GhDNFYB19, and a homeodomain zipper member GhHDZ5. Overall, our phosphoproteomic research advances the understanding of fiber development controlled by BR signal pathways especially through GhSKs, and also offers numbers of target proteins for improving cotton fiber quality.展开更多
目的:比较鼻咽癌(nasopharyngeal carcinoma,NPC)组织与正常鼻咽上皮组织磷酸化蛋白质组差异,筛选差异磷酸化蛋白质,为揭示NPC的发病机制提供依据。方法:采用双向凝胶电泳技术(2-DE)分离NPC组织与正常鼻咽上皮组织的总蛋白质,蛋白质转...目的:比较鼻咽癌(nasopharyngeal carcinoma,NPC)组织与正常鼻咽上皮组织磷酸化蛋白质组差异,筛选差异磷酸化蛋白质,为揭示NPC的发病机制提供依据。方法:采用双向凝胶电泳技术(2-DE)分离NPC组织与正常鼻咽上皮组织的总蛋白质,蛋白质转膜后与抗酪氨酸磷酸化抗体进行Western印迹分析,图像分析识别差异磷酸化蛋白质点,电喷雾-四极杆-串联质谱(ESI-Q-TOF MS/MS)鉴定差异的酪氨酸磷酸化蛋白质,采用NetPhos软件预测蛋白质的酪氨酸磷酸化位点,并采用生物信息学方法对差异磷酸化蛋白质的功能和亚细胞定位进行分析。采用Western印迹检测差异蛋白质(phosphatidylethanolamine-binding protein 1)在正常鼻咽黏膜组织和鼻咽癌组织的总蛋白质中的磷酸化水平。结果:建立了NPC组织与正常鼻咽上皮组织的酪氨酸磷酸化蛋白质表达谱,识别了25个差异酪氨酸磷酸化蛋白质,共鉴定了13个差异酪氨酸磷酸化蛋白质,其中7个蛋白质的酪氨酸磷酸化水平在NPC组织中增强,而6个蛋白质的酪氨酸磷酸化水平降低。NetPhos软件预测和生物信息学分析结果显示,13个差异蛋白质均存在酪氨酸磷酸化位点,其功能涉及物质代谢、细胞结构、细胞防御以及信号转导。与正常鼻咽黏膜组织相比较,差异蛋白phosphatidylethanolamine-binding protein 1在鼻咽癌组织中磷酸化表达水平下调。结论:鉴定了13个可能与NPC发病相关的酪氨酸磷酸化蛋白质,为揭示NPC发病机制提供了科学论依据。展开更多
The most common phenotype induced by the endosymbiont Wolbachia in in-sects is cytoplasmic incompatibility,where none or fewer progenies can be produced when Wolbachia-infected males mate with uninfected females.This ...The most common phenotype induced by the endosymbiont Wolbachia in in-sects is cytoplasmic incompatibility,where none or fewer progenies can be produced when Wolbachia-infected males mate with uninfected females.This suggests that some modi-fications are induced in host sperms during spermatogenesis by Wolbachia.To identify the proteins whose phosphorylation states play essential roles in male reproduction in Drosophila melanogaster,we applied isobaric tags for relative and absolute quantitation(iTRAQ)-based proteomic strategy combined with titanium dioxide(TiO2)enrichment to compare the phosphoproteome of Wolbachia-infected with that of uninfected male re-productive systems in D.melanogaster.We identified 182 phosphopeptides,defining 140 phosphoproteins,that have at least a 1.2 fold change in abundance with a P-value of<0.05.Most of the differentially abundant phosphoproteins(DAPPs)were associated with micro-tubule cytoskeleton organization and spermatid differentiation.The DAPPs included pro-teins already known to be associated with spermatogenesis,as well as many not previously studied during this process.Six genes coding for DAPPs were knocked down,respectively,in Wolbachia-free fly testes.Among them,Slmap knockdown caused the most severe dam-age in spermatogenesis,with no mature sperm observed in seminal vesicles.Immunoflu-orescence staining showed that the formation of individualization complex composed of actin cones was completely disrupted.These results suggest that Wolbachia may induce wide changes in the abundance of phosphorylated proteins which are closely related to male reproduction.By identifying phospho-modulated proteins we also provide a signifi-cant candidate set for future studies on their roles in spermatogenesis.展开更多
Phosphorylation plays crucial parts in lenticular biological function.Getting knowledge of region-resolved phosphoproteome contributes to better comprehending the pathogenesis.Here,we prepared the hybrid metal organic...Phosphorylation plays crucial parts in lenticular biological function.Getting knowledge of region-resolved phosphoproteome contributes to better comprehending the pathogenesis.Here,we prepared the hybrid metal organic frameworks(HMOFs)for probing the region-resolved heterogeneity of phosphoproteome in human lens.1334 phosphosites corresponding to 564 phosphoproteins,1160 phosphosites corresponding to 316 phosphoproteins and 517 phosphosites corresponding to 205 phosphoproteins were identified in capsule,cortex and nucleus,respectively,providing the relatively extensive distribution mapping of phosphorylation in human lens for the first time.The label-free quantification experiments and principal component analysis presented differential expression of phopshoproteins in three subregions.For instance,α-crystallin,β-crystallin and fibrillin-1 closely associated with cataract and Marfan syndrome showed disparate spatial distribution.The preferential phosphoproteins in capsule,cortex and nucleus were involved in cytoskeleton organization,metabolic process and lens development in camera-type eye,respectively.This work first provided a general overview of region-resolved phosphoproteome of human lens.展开更多
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.
文摘Background：The molecular mechanisms underlying the endometriosis are still not completely understood.In order to test the hypothesis that the approaches in phosphoproteomics might contribute to the identification of key biomarkers to assess disease pathogenesis and drug targets,we carried out a phosphoproteomics analysis of human endometrium.Methods：A large-scale differential phosphoproteome analysis,using peptide enrichment of titanium dioxide purify and sequential elution from immobilized metal affinity chromatography with linear trap quadrupole-tandem mass spectrometry,was performed in endometrium tissues from 8 women with or without endometriosis.Results：The phosphorylation profiling of endometrium from endometriosis patients had been obtained,and found that identified 516 proteins were modified at phosphorylation level during endometriosis.Gene ontology annotation analysis showed that these proteins were enriched in cellular processes of binding and catalytic activity.Further pathway analysis showed that ribosome pathway and focal adhesion pathway were the top two pathways,which might be deregulated during the development of endometriosis.Conclusions：That large-scale phosphoproteome quantification has been successfully identified in endometrium tissues of women with or without endometriosis will provide new insights to understand the molecular mechanisms of the development of endometriosis.
基金supported by the National Key R&D Program of China(Grant No.2016YFD0101003)the Heilongjiang Provincial Outstanding Youth Science Foundation,China(Grant No.JC2017008)
文摘De-etiolation consists of a series of developmental and physiological changes that a plant undergoes in response to light.During this process light,an important environmental signal,triggers the inhibition of mesocotyl elongation and the production of photosynthetically active chloroplasts,and etiolated leaves transition from the"sink"stage to the"source"stage.De-etiolation has been extensively studied in maize(Zea mays L.).However,little is known about how this transition is regulated.In this study,we described a quantitative proteomic and phosphoproteomic atlas of the de-etiolation process in maize.We identified 16,420 proteins in proteome,among which 14,168 proteins were quantified.In addition,8746 phosphorylation sites within 3110 proteins were identified.From the combined proteomic and phosphoproteomic data,we identified a total of 17,436 proteins.Only 7.0%(998/14,168)of proteins significantly changed in abundance during de-etiolation.In contrast,26.6%of phosphorylated proteins exhibited significant changes in phosphorylation level;these included proteins involved in gene expression and homeostatic pathways and rate-limiting enzymes involved in photosynthetic light and carbon reactions.Based on phosphoproteomic analysis,34.0%(1057/3110)of phosphorylated proteins identified in this study contained more than 2 phosphorylation sites,and 37 proteins contained more than 16 phosphorylation sites,indicating that multi-phosphorylation is ubiquitous during the de-etiolation process.Our results suggest that plants might preferentially regulate the level of posttranslational modifications(PTMs)rather than protein abundance for adapting to changing environments.The study of PTMs could thus better reveal the regulation of de-etiolation.
文摘We now know that 11 different families of cyclic nucleotide phosphodiesterases(PDEs) are expressed in mammalian species. Most of these families contain multiple gene products and most of the genes utilize alternative splicing or alternative start sites to encode more than one RNA/protein.However,specific functions for these different PDEs have not yet been identified in most cell types despite the fact that selective inhibitors to most of the PDE families are available. Conventional approaches to study PDE function typically rely on measurements of global cAMP,or general increases in cAMP-dependent protein kinase A(PKA),or exchange protein activated by cAMP(EPAC) activity.Although newer approaches utilizing subcellularly-targeted FRET reporter sensors have helped to define more compartmentalized regulation of cAMP,PKA,and EPAC,they have limited ability to link this regulation to downstream effector molecules and biological functions. To address this problem,we have begun to use an unbiased,mass spectrometry-based approach coupled with treatment using PDE isozyme-selective inhibitors to characterize the phosphoproteomes of the ″ functional pools″ of cAMP that are regulated by specific cAMP-PDEs(the PDE-regulated phosphoproteomes). In MA-10 Leydig cells we find that in order to detect appreciable increased in either phosphorylation or steroid production,one needs to inhibit both PDE 4 and PDE 8 activity.Using this combination of inhibitors,we find large PDE inhibitor-induced changes in many different proteins that modulate steroid trafficking and biosynthesis. The data are consistent with the idea that cAMP serves to coordinate hormone stimulation of steroid production by altering the phosphorylation of many different proteins at multiple points in the overall pathway rather than just controlling a single rate limiting step. It seems quite likely that many of the proteins phosphorylated in this cell type in response to PDE inhibition,will also be regulated by cAMP in many other cell types.Similarly,in Jurkat ce
基金supported by the National Natural Science Foundation of China(31971987 and 31601067)。
文摘Brassinosteroid(BR), a steroid phytohormone, whose signaling transduction pathways include a series of phosphorylation and dephosphorylation events, and GSK3 s are the main negative regulator kinases. BRs have been shown to play vital roles in cotton fiber elongation. However, the underlying mechanism is still elusive. In this study, fibers of a BR-defective mutant Pagoda 1(pag1), and its corresponding wild-type(ZM24) were selected for a comparative global phosphoproteome analysis at critical developmental time points: fast-growing stage(10 days after pollination(DPA)) and secondary cell wall synthesis stage(20DPA). Based on the substrate characteristics of GSK3, 900 potential substrates were identified. Their GO and KEGG annotation results suggest that BR functions in fiber development by regulating GhSKs(GSK3s of Gossypium hirsutum L.) involved microtubule cytoskeleton organization, and pathways of glucose, sucrose and lipid metabolism. Further experimental results revealed that among the GhSK members identified, GhSK13 not only plays a role in BR signaling pathway, but also functions in developing fiber by respectively interacting with an AP2-like ethylene-responsive factor GhAP2L, a nuclear transcription factor GhDNFYB19, and a homeodomain zipper member GhHDZ5. Overall, our phosphoproteomic research advances the understanding of fiber development controlled by BR signal pathways especially through GhSKs, and also offers numbers of target proteins for improving cotton fiber quality.
文摘目的:比较鼻咽癌(nasopharyngeal carcinoma,NPC)组织与正常鼻咽上皮组织磷酸化蛋白质组差异,筛选差异磷酸化蛋白质,为揭示NPC的发病机制提供依据。方法:采用双向凝胶电泳技术(2-DE)分离NPC组织与正常鼻咽上皮组织的总蛋白质,蛋白质转膜后与抗酪氨酸磷酸化抗体进行Western印迹分析,图像分析识别差异磷酸化蛋白质点,电喷雾-四极杆-串联质谱(ESI-Q-TOF MS/MS)鉴定差异的酪氨酸磷酸化蛋白质,采用NetPhos软件预测蛋白质的酪氨酸磷酸化位点,并采用生物信息学方法对差异磷酸化蛋白质的功能和亚细胞定位进行分析。采用Western印迹检测差异蛋白质(phosphatidylethanolamine-binding protein 1)在正常鼻咽黏膜组织和鼻咽癌组织的总蛋白质中的磷酸化水平。结果:建立了NPC组织与正常鼻咽上皮组织的酪氨酸磷酸化蛋白质表达谱,识别了25个差异酪氨酸磷酸化蛋白质,共鉴定了13个差异酪氨酸磷酸化蛋白质,其中7个蛋白质的酪氨酸磷酸化水平在NPC组织中增强,而6个蛋白质的酪氨酸磷酸化水平降低。NetPhos软件预测和生物信息学分析结果显示,13个差异蛋白质均存在酪氨酸磷酸化位点,其功能涉及物质代谢、细胞结构、细胞防御以及信号转导。与正常鼻咽黏膜组织相比较,差异蛋白phosphatidylethanolamine-binding protein 1在鼻咽癌组织中磷酸化表达水平下调。结论:鉴定了13个可能与NPC发病相关的酪氨酸磷酸化蛋白质,为揭示NPC发病机制提供了科学论依据。
基金supported by the National Natural Science Foundation of China(no.31672352,31872288).
文摘The most common phenotype induced by the endosymbiont Wolbachia in in-sects is cytoplasmic incompatibility,where none or fewer progenies can be produced when Wolbachia-infected males mate with uninfected females.This suggests that some modi-fications are induced in host sperms during spermatogenesis by Wolbachia.To identify the proteins whose phosphorylation states play essential roles in male reproduction in Drosophila melanogaster,we applied isobaric tags for relative and absolute quantitation(iTRAQ)-based proteomic strategy combined with titanium dioxide(TiO2)enrichment to compare the phosphoproteome of Wolbachia-infected with that of uninfected male re-productive systems in D.melanogaster.We identified 182 phosphopeptides,defining 140 phosphoproteins,that have at least a 1.2 fold change in abundance with a P-value of<0.05.Most of the differentially abundant phosphoproteins(DAPPs)were associated with micro-tubule cytoskeleton organization and spermatid differentiation.The DAPPs included pro-teins already known to be associated with spermatogenesis,as well as many not previously studied during this process.Six genes coding for DAPPs were knocked down,respectively,in Wolbachia-free fly testes.Among them,Slmap knockdown caused the most severe dam-age in spermatogenesis,with no mature sperm observed in seminal vesicles.Immunoflu-orescence staining showed that the formation of individualization complex composed of actin cones was completely disrupted.These results suggest that Wolbachia may induce wide changes in the abundance of phosphorylated proteins which are closely related to male reproduction.By identifying phospho-modulated proteins we also provide a signifi-cant candidate set for future studies on their roles in spermatogenesis.
基金financially supported by National Key R&D Program of China(No.2018YFA0507501)the National Natural Science Foundation of China(Nos.22074019,21425518 and 22004017)Shanghai Sailing Program(No.20YF1405300)。
文摘Phosphorylation plays crucial parts in lenticular biological function.Getting knowledge of region-resolved phosphoproteome contributes to better comprehending the pathogenesis.Here,we prepared the hybrid metal organic frameworks(HMOFs)for probing the region-resolved heterogeneity of phosphoproteome in human lens.1334 phosphosites corresponding to 564 phosphoproteins,1160 phosphosites corresponding to 316 phosphoproteins and 517 phosphosites corresponding to 205 phosphoproteins were identified in capsule,cortex and nucleus,respectively,providing the relatively extensive distribution mapping of phosphorylation in human lens for the first time.The label-free quantification experiments and principal component analysis presented differential expression of phopshoproteins in three subregions.For instance,α-crystallin,β-crystallin and fibrillin-1 closely associated with cataract and Marfan syndrome showed disparate spatial distribution.The preferential phosphoproteins in capsule,cortex and nucleus were involved in cytoskeleton organization,metabolic process and lens development in camera-type eye,respectively.This work first provided a general overview of region-resolved phosphoproteome of human lens.
