Rice grows in flooded paddy fields and takes up ammonium as the preferred nitrogen （N） source. Ammonium uptake is facilitated by a family of integral membrane proteins known as ammonium transporters found in all dom...Rice grows in flooded paddy fields and takes up ammonium as the preferred nitrogen （N） source. Ammonium uptake is facilitated by a family of integral membrane proteins known as ammonium transporters found in all domains of life. However, the molecular mechanism and functional characteristics of the ammonium transporters （AMT） in rice have not been determined in detail yet. In this review, we report a genome-wide search for AMT genes in rice, resulting in the increase of the number of potential AMT proteins to at least 12, including members of both the alpha and beta sub-groups. Analysis of the predicted protein sequences for the 12 OsAMT proteins identified many conserved phosphorylation sites in both the alpha and beta group members, which could potentially play a role in controlling the activity of the transporters. Present knowledge of the expression of rice AMT genes is also summarized in detail. Future studies should focus on the structural and functional characteristics of OsAMT proteins to provide insight into the mechanism of ammonium uptake and its regulation in rice. Such research could improve utilization and decrease wastage of N fertilizer in rice cultivation.展开更多
Polyolefins such as polyethylene(PE)are one of the largest-scale synthetic plastics and play a key role in modern society.However,polyethylene is extremely inert to chemical recycling owing to its lack of chemical fun...Polyolefins such as polyethylene(PE)are one of the largest-scale synthetic plastics and play a key role in modern society.However,polyethylene is extremely inert to chemical recycling owing to its lack of chemical functionality and low polarity,making it one of the most challenging environmental hazards globally.Herein,we developed a phosphorylated CeO_(2)catalyst by an organophosphate precursor and featured efficient photocatalysis of low-density polyethylene(LDPE)without the acid or alkaline pre-treatment.Compared to pristine CeO_(2),the surface phosphorylation allows to introduce Brønsted acid sites,which facilitate to form carbonium ions on LDPE via protonation.In addition,the suitable band structure of the phosphorylated CeO_(2)catalyst enables efficient photoabsorption and generates reactive oxygen species,leading to the C–C bond cleavage of LDPE.As a result,the phosphorylated CeO_(2)catalyst exhibited an outstanding carbon conversion rate of>94%after 48 h of photocatalysis under 50 mW/cm^(2)of simulated sunlight,with a high CO_(2)product selectivity of>99%.Furthermore,the PE microparticles with sizes larger than 10μm released from LDPE plastic wrap were directly and completely degraded by photocatalysis within 12 h,suggesting an attractive and environmentally benign strategy of utilizing solar energy-based photocatalysis for reducing potential hazards of LDPE plastic trashes.展开更多
In eukaryotes,protein phosphorylation is specifically catalyzed by numerous protein kinases(PKs),faithfully orchestrates various biological processes,and reversibly determines cellular dynamics and plasticity.Here we ...In eukaryotes,protein phosphorylation is specifically catalyzed by numerous protein kinases(PKs),faithfully orchestrates various biological processes,and reversibly determines cellular dynamics and plasticity.Here we report an updated algorithm of Group-based Prediction System(GPS)5.0 to improve the performance for predicting kinase-specific phosphorylation sites(p-sites).Two novel methods,position weight determination(PWD)and scoring matrix optimization(SMO),were developed.Compared with other existing tools,GPS 5.0 exhibits a highly competitive accuracy.Besides serine/threonine or tyrosine kinases,GPS 5.0 also supports the prediction of dual-specificity kinase-specific p-sites.In the classical module of GPS 5.0,617 individual predictors were constructed for predicting p-sites of 479 human PKs.To extend the application of GPS5.0,a species-specific module was implemented to predict kinase-specific p-sites for 44,795 PKs in161 eukaryotes.The online service and local packages of GPS 5.0 are freely available for academic research at http://gps.biocuckoo.cn.展开更多
The purpose of this work is to enhance KinasePhos,a machine learning-based kinasespecific phosphorylation site prediction tool.Experimentally verified kinase-specific phosphorylation data were collected from PhosphoSi...The purpose of this work is to enhance KinasePhos,a machine learning-based kinasespecific phosphorylation site prediction tool.Experimentally verified kinase-specific phosphorylation data were collected from PhosphoSitePlus,UniProtKB,the GPS 5.0,and Phospho.ELM.In total,41,421 experimentally verified kinase-specific phosphorylation sites were identified.A total of 1380 unique kinases were identified,including 753 with existing classification information from KinBase and the remaining 627 annotated by building a phylogenetic tree.Based on this kinase classification,a total of 771 predictive models were built at the individual,family,and group levels,using at least 15 experimentally verified substrate sites in positive training datasets.The improved models demonstrated their effectiveness compared with other prediction tools.For example,the prediction of sites phosphorylated by the protein kinase B,casein kinase 2,and protein kinase A families had accuracies of 94.5%,92.5%,and 90.0%,respectively.The average prediction accuracy for all 771 models was 87.2%.For enhancing interpretability,the SHapley Additive exPlanations(SHAP)method was employed to assess feature importance.The web interface of KinasePhos 3.0 has been redesigned to provide comprehensive annotations of kinase-specific phosphorylation sites on multiple proteins.Additionally,considering the large scale of phosphoproteomic data,a downloadable prediction tool is available at https://awi.cuhk.edu.cn/KinasePhos/download.html or https://github.com/tom-209/KinasePhos-3.0-executable-file.展开更多
为深入研究小反刍兽疫病毒(peste des petits ruminants virus,PPRV)P蛋白对病毒复制的影响,以小反刍兽疫病毒Nigeria75/1株为研究对象,通过RT-PCR法扩增P基因,将扩增出的P基因克隆到pGEX-6P-1原核表达载体中,成功构建pGEX-6P-1-PPRV-P...为深入研究小反刍兽疫病毒(peste des petits ruminants virus,PPRV)P蛋白对病毒复制的影响,以小反刍兽疫病毒Nigeria75/1株为研究对象,通过RT-PCR法扩增P基因,将扩增出的P基因克隆到pGEX-6P-1原核表达载体中,成功构建pGEX-6P-1-PPRV-P表达载体,测序鉴定无误后转化至表达宿主菌BL21(DE3)plysS中进行IPTG诱导表达,并通过在线软件预测了P蛋白的磷酸化位点。结果显示,pGEX-6P-1-PPRV-P重组菌在IPTG浓度1.0mmol/L时经37℃诱导4h,目的基因可正确表达,并以可溶性的形式存在。经Western-blot鉴定,目的蛋白可与PPRV Nigeria75/1株病毒小鼠阳性血清发生特异性的免疫印迹反应,证明表达的蛋白具有较好的反应原性。经综合预测分析,可能被磷酸化的位点有46个,其中PKC、PKA、CKII/CKI、cdc2可能作用的位点分别为15个、7个、10个、6个,其他激酶作用位点可能为8个。结果表明,P蛋白的克隆表达及磷酸化位点的成功预测为小反刍兽疫病毒的深入研究奠定了基础。展开更多
As the preferred nitrogen(N)source,ammonium(NH_(4)^(+))contributes to plant growth and development and fruit quality.In plants,NH 4+uptake is facilitated by a family of NH_(4)^(+) transporters(AMT).However,the molecul...As the preferred nitrogen(N)source,ammonium(NH_(4)^(+))contributes to plant growth and development and fruit quality.In plants,NH 4+uptake is facilitated by a family of NH_(4)^(+) transporters(AMT).However,the molecular mechanisms and functional characteristics of the AMT genes in peach have not been mentioned yet.In this present study,excess NH_(4)^(+) stress severely hindered shoot growth and root elongation,accompanied with reduced mineral accumulation,decreased leaf chlorophyll concentration,and stunned photosynthetic performance.In addition,we identified 14 putative AMT genes in peach(PpeAMT).Expression analysis showed that PpeAMT genes were differently expressed in peach leaves,stems and roots,and were distinctly regulated by external NH_(4)^(+) supplies.Putative cis-elements involved in abiotic stress adaption,Ca^(2+) response,light and circadian rhythms regulation,and seed development were observed in the promoters of the PpeAMT family genes.Phosphorylation analysis of residues within the C-terminal of PpeAMT proteins revealed many conserved phosphorylation residues in both the AMT1 and AMT2 subfamily members,which could potentially play roles in controlling the NH 4+transport activities.This study provides gene resources to study the biological function of AMT proteins in peach,and reveals molecular basis for NH_(4)^(+) uptake and N nutrition mechanisms of fruit trees.展开更多
Sequence similarities were found between protein and DNA sequences encoding certain part of conserved variable immunoglobulin domains (i.e. conserved IgV) and phosphorylation sites. Hypermutation motifs were then indi...Sequence similarities were found between protein and DNA sequences encoding certain part of conserved variable immunoglobulin domains (i.e. conserved IgV) and phosphorylation sites. Hypermutation motifs were then indicated in the majority of the corresponding non-IgV nucleotide sequences. According to database confirmations or double prediction of phosphorylation sites, 80% of the selected human and mouse IgV-related phosphorylation sites or their highly probable candidates exhibited substrate relationship to ataxia-telangiectasia-mutated kinase known as ATM. In accordance with literature data, inactivation of ATM by mutations can participate in the mechanisms of carcinogenesis, neurodegeneration and possibly also in aging. In agreement with this relationship, some of the selected IgV-/ATM-related segments formed molecules specifically involved in carcinogenesis. The selected IgV-related sequence segments were also similar to certain segments of higher plants containing immunoglobulin-like repeats and related regions. Bioinformatic analysis of some selected plant sequences then indicated the presence of catalytic domains composing serine/threonine/tyrosine receptor/receptor-like kinases, which are considered important structures for evolution of very early and part of later Ig-domain-related immunity. The analyzed conserved domain similarities also suggested certain interesting structural and phylogenic relationships, which need to be further investigated. This review in fact briefly summarizes the findings on the subject from the last twenty years.展开更多
The phosphorylation sites of two phosphorylated proteins, bovine β-casein and myelin basic protein (MBP), were identified by high performance liquid chromatography-electrospray ionization-quadrupole ion trap mass spe...The phosphorylation sites of two phosphorylated proteins, bovine β-casein and myelin basic protein (MBP), were identified by high performance liquid chromatography-electrospray ionization-quadrupole ion trap mass spectrometry (HPLC-ESI-QITMS). The tryptic digest of each protein was separated by HPLC, the molecular weight of each peptide was determined by ESI-QITMS on line, and MS/MS spectrum of each peptide was simultaneously obtained by the combination of collision-induced desorption (CID) technique and tandem mass spectrometry (MS/MS) of QITMS. The phosphorylated peptide was identified by looking into whether the difference between the observed and predicted molecular weights of a peptide is 80 u or its integral multiple. Then the phosphorylation site was identified through manual interpretation of the MS/MS spectrum of the phosphorylated peptide or automatic SEQUEST data base-searching.展开更多
TRAF4 is a unique member of TRAF family,which is es-sential for innate immune response,nervous system and other systems.In addition to being an adaptor protein,TRAF4 was identifi ed as a regulator protein in recent st...TRAF4 is a unique member of TRAF family,which is es-sential for innate immune response,nervous system and other systems.In addition to being an adaptor protein,TRAF4 was identifi ed as a regulator protein in recent studies.We have determined the crystal structure of TRAF domain of TRAF4(residues 292-466)at 2.60Åresolution by X-ray crystallography method.The trimericly assembled TRAF4 resembles a mushroom shape,containing a super helical“stalk”which is made of three right-handed intertwinedαhelixes and a C-terminal“cap”,which is divided at resi-due L302 as a boundary.Similar to other TRAFs,both intermolecular hydrophobic interaction in super helical“stalk”and hydrogen bonds in“cap”regions contribute directly to the formation of TRAF4 trimer.However,differ-ing from other TRAFs,there is an additional fl exible loop(residues 421-426),which contains a previously identifi ed phosphorylated site S426 exposing on the surface.This S426 was reported to be phosphorylated by IKKαwhich is the pre-requisite for TRAF4-NOD2 complex formation and thus to inhibit NOD2-induced NF-κB activation.Therefore,the crystal structure of TRAF4-TRAF is valuable for under-standing its molecular basis for its special function and provides structural information for further studies.展开更多
基金supported by the China Postdoctoral Science Foundation (Grant No. 20070421031)the National Basic Research Program of China (Grant No. 2007CB109303)Knowledge Innovation Project of the Chinese Academy of Sciences (Grant No. KSCX2-YW-N-002)
文摘Rice grows in flooded paddy fields and takes up ammonium as the preferred nitrogen （N） source. Ammonium uptake is facilitated by a family of integral membrane proteins known as ammonium transporters found in all domains of life. However, the molecular mechanism and functional characteristics of the ammonium transporters （AMT） in rice have not been determined in detail yet. In this review, we report a genome-wide search for AMT genes in rice, resulting in the increase of the number of potential AMT proteins to at least 12, including members of both the alpha and beta sub-groups. Analysis of the predicted protein sequences for the 12 OsAMT proteins identified many conserved phosphorylation sites in both the alpha and beta group members, which could potentially play a role in controlling the activity of the transporters. Present knowledge of the expression of rice AMT genes is also summarized in detail. Future studies should focus on the structural and functional characteristics of OsAMT proteins to provide insight into the mechanism of ammonium uptake and its regulation in rice. Such research could improve utilization and decrease wastage of N fertilizer in rice cultivation.
基金the following funding agencies for supporting this work: the National Natural Science Foundation of China (22025502, U23A20552, 22379026, 22222901, 22175022)the Natural Science Foundation of Shanghai (23ZR1407000)the Science and Technology Commission of Shanghai Municipality (21DZ1206800)
文摘Polyolefins such as polyethylene(PE)are one of the largest-scale synthetic plastics and play a key role in modern society.However,polyethylene is extremely inert to chemical recycling owing to its lack of chemical functionality and low polarity,making it one of the most challenging environmental hazards globally.Herein,we developed a phosphorylated CeO_(2)catalyst by an organophosphate precursor and featured efficient photocatalysis of low-density polyethylene(LDPE)without the acid or alkaline pre-treatment.Compared to pristine CeO_(2),the surface phosphorylation allows to introduce Brønsted acid sites,which facilitate to form carbonium ions on LDPE via protonation.In addition,the suitable band structure of the phosphorylated CeO_(2)catalyst enables efficient photoabsorption and generates reactive oxygen species,leading to the C–C bond cleavage of LDPE.As a result,the phosphorylated CeO_(2)catalyst exhibited an outstanding carbon conversion rate of>94%after 48 h of photocatalysis under 50 mW/cm^(2)of simulated sunlight,with a high CO_(2)product selectivity of>99%.Furthermore,the PE microparticles with sizes larger than 10μm released from LDPE plastic wrap were directly and completely degraded by photocatalysis within 12 h,suggesting an attractive and environmentally benign strategy of utilizing solar energy-based photocatalysis for reducing potential hazards of LDPE plastic trashes.
基金Special Project on Precision Medicine under the National Key R&D Program of China(Grant Nos.2017YFC0906600 and 2018YFC0910500)National Natural Science Foundation of China(Grant Nos.31671360,81701567,and 31801095)+2 种基金National Program for Support of Top-Notch Young Professionals,Changjiang Scholars Program of Chinasupported by the program for HUST Academic Frontier Youth Team,Fundamental Research Funds for the Central Universities,China(Grant Nos.2017KFXKJC001 and 2019kfy RCPY043)China Postdoctoral Science Foundation(Grant Nos.2018M642816 and 2018M632870)
文摘In eukaryotes,protein phosphorylation is specifically catalyzed by numerous protein kinases(PKs),faithfully orchestrates various biological processes,and reversibly determines cellular dynamics and plasticity.Here we report an updated algorithm of Group-based Prediction System(GPS)5.0 to improve the performance for predicting kinase-specific phosphorylation sites(p-sites).Two novel methods,position weight determination(PWD)and scoring matrix optimization(SMO),were developed.Compared with other existing tools,GPS 5.0 exhibits a highly competitive accuracy.Besides serine/threonine or tyrosine kinases,GPS 5.0 also supports the prediction of dual-specificity kinase-specific p-sites.In the classical module of GPS 5.0,617 individual predictors were constructed for predicting p-sites of 479 human PKs.To extend the application of GPS5.0,a species-specific module was implemented to predict kinase-specific p-sites for 44,795 PKs in161 eukaryotes.The online service and local packages of GPS 5.0 are freely available for academic research at http://gps.biocuckoo.cn.
基金The authors express their gratitude toward all database developers mentioned and quoted in this article for their important work and the data they shared.The author also would like to thank users for their comments and suggestions on the previous version of KinasePhos.This work was supported by the National Natural Science Foundation of China(Grant No.32070659)the Science,Technology and Innovation Commission of Shenzhen Municipality(Grant No.JCYJ20200109150003938)+1 种基金the Guangdong Province Basic and Applied Basic Research Fund(Grant No.2021A1515012447)the Ganghong Young Scholar Development Fund(Grant No.2021E007),China.This work is supported by the Warshel Institute for Computational Biology funding from Shenzhen City and Longgang District,China.
文摘The purpose of this work is to enhance KinasePhos,a machine learning-based kinasespecific phosphorylation site prediction tool.Experimentally verified kinase-specific phosphorylation data were collected from PhosphoSitePlus,UniProtKB,the GPS 5.0,and Phospho.ELM.In total,41,421 experimentally verified kinase-specific phosphorylation sites were identified.A total of 1380 unique kinases were identified,including 753 with existing classification information from KinBase and the remaining 627 annotated by building a phylogenetic tree.Based on this kinase classification,a total of 771 predictive models were built at the individual,family,and group levels,using at least 15 experimentally verified substrate sites in positive training datasets.The improved models demonstrated their effectiveness compared with other prediction tools.For example,the prediction of sites phosphorylated by the protein kinase B,casein kinase 2,and protein kinase A families had accuracies of 94.5%,92.5%,and 90.0%,respectively.The average prediction accuracy for all 771 models was 87.2%.For enhancing interpretability,the SHapley Additive exPlanations(SHAP)method was employed to assess feature importance.The web interface of KinasePhos 3.0 has been redesigned to provide comprehensive annotations of kinase-specific phosphorylation sites on multiple proteins.Additionally,considering the large scale of phosphoproteomic data,a downloadable prediction tool is available at https://awi.cuhk.edu.cn/KinasePhos/download.html or https://github.com/tom-209/KinasePhos-3.0-executable-file.
基金This work was supported by the National Key R&D Program of China(2019YFD1000500,2016YFD0600106)China Agriculture Research System(CARS-29-16),the Agricultural Variety Improvement Project of Shandong Province(2019LZGC009)the Key R&D Program of Shandong Province(GG201809260221,2019GSF1070952,018JHZ006).
文摘As the preferred nitrogen(N)source,ammonium(NH_(4)^(+))contributes to plant growth and development and fruit quality.In plants,NH 4+uptake is facilitated by a family of NH_(4)^(+) transporters(AMT).However,the molecular mechanisms and functional characteristics of the AMT genes in peach have not been mentioned yet.In this present study,excess NH_(4)^(+) stress severely hindered shoot growth and root elongation,accompanied with reduced mineral accumulation,decreased leaf chlorophyll concentration,and stunned photosynthetic performance.In addition,we identified 14 putative AMT genes in peach(PpeAMT).Expression analysis showed that PpeAMT genes were differently expressed in peach leaves,stems and roots,and were distinctly regulated by external NH_(4)^(+) supplies.Putative cis-elements involved in abiotic stress adaption,Ca^(2+) response,light and circadian rhythms regulation,and seed development were observed in the promoters of the PpeAMT family genes.Phosphorylation analysis of residues within the C-terminal of PpeAMT proteins revealed many conserved phosphorylation residues in both the AMT1 and AMT2 subfamily members,which could potentially play roles in controlling the NH 4+transport activities.This study provides gene resources to study the biological function of AMT proteins in peach,and reveals molecular basis for NH_(4)^(+) uptake and N nutrition mechanisms of fruit trees.
文摘Sequence similarities were found between protein and DNA sequences encoding certain part of conserved variable immunoglobulin domains (i.e. conserved IgV) and phosphorylation sites. Hypermutation motifs were then indicated in the majority of the corresponding non-IgV nucleotide sequences. According to database confirmations or double prediction of phosphorylation sites, 80% of the selected human and mouse IgV-related phosphorylation sites or their highly probable candidates exhibited substrate relationship to ataxia-telangiectasia-mutated kinase known as ATM. In accordance with literature data, inactivation of ATM by mutations can participate in the mechanisms of carcinogenesis, neurodegeneration and possibly also in aging. In agreement with this relationship, some of the selected IgV-/ATM-related segments formed molecules specifically involved in carcinogenesis. The selected IgV-related sequence segments were also similar to certain segments of higher plants containing immunoglobulin-like repeats and related regions. Bioinformatic analysis of some selected plant sequences then indicated the presence of catalytic domains composing serine/threonine/tyrosine receptor/receptor-like kinases, which are considered important structures for evolution of very early and part of later Ig-domain-related immunity. The analyzed conserved domain similarities also suggested certain interesting structural and phylogenic relationships, which need to be further investigated. This review in fact briefly summarizes the findings on the subject from the last twenty years.
文摘The phosphorylation sites of two phosphorylated proteins, bovine β-casein and myelin basic protein (MBP), were identified by high performance liquid chromatography-electrospray ionization-quadrupole ion trap mass spectrometry (HPLC-ESI-QITMS). The tryptic digest of each protein was separated by HPLC, the molecular weight of each peptide was determined by ESI-QITMS on line, and MS/MS spectrum of each peptide was simultaneously obtained by the combination of collision-induced desorption (CID) technique and tandem mass spectrometry (MS/MS) of QITMS. The phosphorylated peptide was identified by looking into whether the difference between the observed and predicted molecular weights of a peptide is 80 u or its integral multiple. Then the phosphorylation site was identified through manual interpretation of the MS/MS spectrum of the phosphorylated peptide or automatic SEQUEST data base-searching.
基金the Ministry of Health of China(grant 2013ZX10004-602)the National Basic Research Program(973 Program)(Nos.2013CB911103,2009DFB30310,2009CB918803 and 2011CB911103)the National Natural Science Foundation of China(Grant Nos.31270795,31200559,31070660 and 31021062).
文摘TRAF4 is a unique member of TRAF family,which is es-sential for innate immune response,nervous system and other systems.In addition to being an adaptor protein,TRAF4 was identifi ed as a regulator protein in recent studies.We have determined the crystal structure of TRAF domain of TRAF4(residues 292-466)at 2.60Åresolution by X-ray crystallography method.The trimericly assembled TRAF4 resembles a mushroom shape,containing a super helical“stalk”which is made of three right-handed intertwinedαhelixes and a C-terminal“cap”,which is divided at resi-due L302 as a boundary.Similar to other TRAFs,both intermolecular hydrophobic interaction in super helical“stalk”and hydrogen bonds in“cap”regions contribute directly to the formation of TRAF4 trimer.However,differ-ing from other TRAFs,there is an additional fl exible loop(residues 421-426),which contains a previously identifi ed phosphorylated site S426 exposing on the surface.This S426 was reported to be phosphorylated by IKKαwhich is the pre-requisite for TRAF4-NOD2 complex formation and thus to inhibit NOD2-induced NF-κB activation.Therefore,the crystal structure of TRAF4-TRAF is valuable for under-standing its molecular basis for its special function and provides structural information for further studies.
